scholarly journals Transposable temperate phages promote the evolution of divergent social strategies inPseudomonas aeruginosapopulations

2019 ◽  
Author(s):  
Siobhán O’Brien ◽  
Rolf Kümmerli ◽  
Steve Paterson ◽  
Craig Winstanley ◽  
Michael A. Brockhurst
Keyword(s):  
Experimental Evolution ◽  
Gene Clusters ◽  
Siderophore Production ◽  
Evolutionary Divergence ◽  
Social Strategies ◽  
Bacterial Genomes ◽  
The Social ◽  
Insertional Inactivation ◽  
Genes Encoding ◽  
Evolutionary Trajectories

AbstractTransposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Here we show, using experimental evolution ofPseudomonas aeruginosain iron-limited and iron-rich environments causing differential expression of siderophore cooperation, that transposable phages promoted divergence into extreme siderophore production phenotypes in iron-limited populations. Iron-limited populations with transposable phages evolved siderophore over-producing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations inpvdgenes, encoding pyoverdine biosynthesis, andpqsgenes, encoding quinolone signaling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.

scholarly journals Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations

2019 ◽  
Vol 286 (1912) ◽  
pp. 20191794 ◽  
Author(s):  
Siobhán O'Brien ◽  
Rolf Kümmerli ◽  
Steve Paterson ◽  
Craig Winstanley ◽  
Michael A. Brockhurst
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Clusters ◽  
Siderophore Production ◽  
Evolutionary Divergence ◽  
Social Strategies ◽  
The Social ◽  
Insertional Inactivation ◽  
Genes Encoding ◽  
Evolutionary Trajectories ◽  
The Cost

Transposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Using experimental evolution of Pseudomonas aeruginosa in iron-limited and iron-rich environments, where the cost of producing cooperative iron-chelating siderophores is high and low, respectively, we show that transposable phages promote divergence into extreme siderophore production phenotypes. Iron-limited populations with transposable phages evolved siderophore overproducing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations in pvd genes, encoding pyoverdine biosynthesis, and pqs genes, encoding quinolone signalling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

The Convent of Santa Clara, the Elite and Social Change in Eighteenth Century Querétaro

2001 ◽  
Vol 33 (2) ◽  
pp. 257-290 ◽  
Author(s):  
ELLEN GUNNARSDÓTTIR
Keyword(s):  
Eighteenth Century ◽  
Seventeenth Century ◽  
Social Change ◽  
Colonial Mexico ◽  
Social Strategies ◽  
The Past ◽  
The Social

This article focuses on the changes that occurred within Querétaro's elite from the late Habsburg to the high Bourbon period in colonial Mexico from the perspective of its relationship to the convent of Santa Clara. It explores how creole elite families of landed background with firm roots in the early seventeenth century, tied together through marriage, entrepreneurship and membership in Santa Clara were slowly pushed out of the city's economic and administrative circles by a new Bourbon elite which broke with the social strategies of the past by not sheltering its daughters in the city's most opulent convent.

scholarly journals Recombinant transfer in the basic genome ofEscherichia coli

2015 ◽  
Vol 112 (29) ◽  
pp. 9070-9075 ◽  
Author(s):  
Purushottam D. Dixit ◽  
Tin Yau Pang ◽  
F. William Studier ◽  
Sergei Maslov
Keyword(s):  
Common Ancestor ◽  
Recipient Cell ◽  
Gene Clusters ◽  
Selective Advantage ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Basic Genome ◽  
Single Base Pair ◽  
Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

scholarly journals Intra- and Interspecies Signaling betweenStreptococcus salivarius and Streptococcus pyogenes Mediated by SalA and SalA1 Lantibiotic Peptides

2001 ◽  
Vol 183 (13) ◽  
pp. 3931-3938 ◽  
Author(s):  
M. Upton ◽  
J. R. Tagg ◽  
P. Wescombe ◽  
H. F. Jenkinson
Keyword(s):  
Streptococcus Pyogenes ◽  
Response Regulator ◽  
Genetic Locus ◽  
Two Component System ◽  
Peptide Modification ◽  
Insertional Inactivation ◽  
Two Component ◽  
Genes Encoding ◽  
Dose Dependent

ABSTRACT Streptococcus salivarius 20P3 produces a 22-amino-acid residue lantibiotic, designated salivaricin A (SalA), that inhibits the growth of a range of streptococci, including all strains ofStreptococcus pyogenes. Lantibiotic production is associated with the sal genetic locus comprisingsalA, the lantibiotic structural gene; salBCTXgenes encoding peptide modification and export machinery proteins; andsalYKR genes encoding a putative immunity protein and two-component sensor-regulator system. Insertional inactivation ofsalB in S. salivarius 20P3 resulted in abrogation of SalA peptide production, of immunity to SalA, and ofsalA transcription. Addition of exogenous SalA peptide tosalB mutant cultures induced dose-dependent expression ofsalA mRNA (0.2 kb), demonstrating that SalA production was normally autoregulated. Inactivation of salR encoding the response regulator of the SalKR two-component system led to reduced production of, and immunity to, SalA. The sal genetic locus was also present in S. pyogenes SF370 (M type 1), but because of a deletion across the salBCT genes, the corresponding lantibiotic peptide, designated SalA1, was not produced. However, in S. pyogenes T11 (M type 4) the sallocus gene complement was apparently complete, and active SalA1 peptide was synthesized. Exogenously added SalA1 peptide from S. pyogenes T11 induced salA1 transcription in S. pyogenes SF370 and in an isogenic S. pyogenes T11salB mutant and salA transcription in S. salivarius 20P3 salB. Thus, SalA and SalA1 are examples of streptococcal lantibiotics whose production is autoregulated. These peptides act as intra- and interspecies signaling molecules, modulating lantibiotic production and possibly influencing streptococcal population ecology in the oral cavity.

scholarly journals Conserved Gene Clusters in Bacterial Genomes Provide Further Support for the Primacy of RNA

1997 ◽  
Vol 45 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Janet L. Siefert ◽  
Kirt A. Martin ◽  
Fadi Abdi ◽  
William R. Widger ◽  
George E. Fox
Keyword(s):  
Gene Clusters ◽  
Bacterial Genomes ◽  
Conserved Gene

Grafinscripties

Lampas ◽  
2021 ◽  
Vol 54 (1) ◽  
pp. 39-65
Author(s):  
Onno van Nijf
Keyword(s):  
Late Antiquity ◽  
Archaic Period ◽  
Social Strategies ◽  
Public And Private ◽  
Content Type ◽  
Frequent Type ◽  
The Social ◽  
Funerary Inscriptions ◽  
Set Up ◽  
Over Time

Abstract This article offers a brief introduction to the most frequent type of inscription: funerary inscriptions or epitaphs. The article offers a chronological overview from the Archaic period to late Antiquity, with an emphasis on Athens. It opens with a brief discussion of the archaeological and ritual contexts in which funerary inscriptions were set up, followed by a discussion of archaic epigrams and the social strategies that lay behind them. This is followed by a discussion of public and private graves that shows how epigraphic habits changed over time. The article continues with a discussion of funerary epigraphic habits outside Athens and closes with a few examples of Christian epitaphs.

scholarly journals Chance, contingency, and necessity in the experimental evolution of ancestral proteins

2020 ◽  
Author(s):  
Victoria Cochran Xie ◽  
Jinyue Pu ◽  
Brian P.H. Metzger ◽  
Joseph W. Thornton ◽  
Bryan C. Dickinson
Keyword(s):  
Protein Evolution ◽  
Experimental Evolution ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Sequence Evolution ◽  
Protein Protein Interaction ◽  
Evolutionary Trajectories ◽  
Historical Moment ◽  
Related Proteins ◽  
Ancestral Protein

SUMMARYThe extent to which chance and contingency shaped the sequence outcomes of protein evolution is largely unknown. To directly characterize the causes and consequences of chance and contingency, we combined directed evolution with ancestral protein reconstruction. By repeatedly selecting a phylogenetic series of ancestral proteins in the B-cell lymphoma-2 family to evolve the same protein-protein interaction specificities that existed during history, we show that contingency and chance interact to make sequence evolution almost entirely unpredictable over the timescale of metazoan evolution. At any historical moment, multiple sets of mutations can alter or maintain specificity, and chance decides which ones occur. Contingency arises because historical sequence substitutions epistatically altered which mutations are compatible with new or ancestral functions. Evolutionary trajectories launched from different ancestors therefore lead to dramatically different outcomes over phylogenetic time, with virtually no mutations occurring repeatedly in distantly related proteins, even under identical selection conditions.

scholarly journals Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues

2020 ◽  
Author(s):  
Sandra A. C. Figueiredo ◽  
Marco Preto ◽  
Gabriela Moreira ◽  
Teresa P. Martins ◽  
Kathleen Abt ◽  
...  
Keyword(s):  
Natural Products ◽  
Fatty Acid ◽  
Isotope Labeling ◽  
Gene Clusters ◽  
New Drugs ◽  
Beta Oxidation ◽  
Bacterial Genomes ◽  
Biosynthetic Gene Clusters ◽  
Apparent Lack ◽  
Massive Sequencing

Natural products have an important role in several human activities, most notably as sources of new drugs. In recent years, massive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a large number of gene clusters that likely incorporate fatty acid-derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent lack of a functional beta-oxidation pathway in cyanobacteria to achieve efficient stable-isotope labeling of their fatty acid-derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids – the nocuolactylates.

scholarly journals Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli

2018 ◽  
Author(s):  
Krithika Rajagopalan ◽  
Jonathan Dworkin
Keyword(s):  
Biochemical Characterization ◽  
Regulatory Protein ◽  
Biochemical Properties ◽  
Bacterial Genomes ◽  
Phosphatase Inhibitors ◽  
E Coli ◽  
Specificity And Sensitivity ◽  
Genes Encoding ◽  
Number Of Bacteria

AbstractIn bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such asE. coli,which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C phosphatases. These proteins, called eSTPs (eukaryotic-like Ser/Thr phosphatases), have been identified in a number of bacteria, but not inE. coli.Here, we describe a previously unknown eSTP encoded by anE. coliORF,yegK,and characterize its biochemical properties including its kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely relatedE. colistrains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon.ImportanceRegulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria including the model Gram-negative bacteriumE. colidemonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported inE. coli, no partner Ser/Thrphosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.

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