New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina

ABSTRACTThe symbiotic association between aphids (Homoptera) andBuchnera aphidicola(Gammaproteobacteria) started about 100 to 200 million years ago. As a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. The downsize genome process starts when the bacterium enters the host and will probably end with its extinction and replacement by another healthier bacterium or with the establishment of metabolic complementation between two or more bacteria. Nowadays, several complete genomes ofBuchnera aphidicolafrom four different aphid species (Acyrthosiphon pisum,Schizaphis graminum,Baizongia pistacea, andCinara cedri) have been fully sequenced.C. cedribelongs to the subfamily Lachninae and harbors two coprimary bacteria that fulfill the metabolic needs of the whole consortium:B. aphidicolawith the smallest genome reported so far and “CandidatusSerratia symbiotica.” In addition,Cinara tujafilina, another member of the subfamily Lachninae, closely related toC. cedri, also harbors “Ca.Serratia symbiotica” but with a different phylogenetic status than the one fromC. cedri. In this study, we present the complete genome sequence ofB. aphidicolafromC. tujafilinaand the phylogenetic analysis and comparative genomics with the otherBuchneragenomes. Furthermore, the gene repertoire of the last common ancestor has been inferred, and the evolutionary history of the metabolic losses that occurred in the different lineages has been analyzed. Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts.

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Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola : bacterial genome helps define species and evolutionary relationships in aphids

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2008.0679 ◽

2008 ◽

Vol 276 (1654) ◽

pp. 187-196 ◽

Cited By ~ 71

Author(s):

Emmanuelle Jousselin ◽

Yves Desdevises ◽

Armelle Coeur d'acier

Keyword(s):

Species Delimitation ◽

Evolutionary History ◽

Bacterial Genome ◽

Specific Interaction ◽

Essential Amino Acids ◽

Buchnera Aphidicola ◽

Species Definition ◽

Taxonomic Level ◽

History Of ◽

Definition Of

Aphids harbour an obligatory symbiont, Buchnera aphidicola , providing essential amino acids not supplied by their diet. These bacteria are transmitted vertically and phylogenic analyses suggest that they have ‘cospeciated’ with their hosts. We investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus Brachycaudus . We used DNA-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and Buchnera species and to infer association patterns without the presumption of a specific interaction. Our results call into question certain ‘taxonomic’ species of Brachycaudus and suggest that B. aphidicola has diversified into independently evolving entities, each specific to a ‘phylogenetic’ Brachycaudus species. We also found that Buchnera and their hosts simultaneously diversified, in parallel. These results validate the use of Buchnera DNA data for inferring the evolutionary history of their host. The Buchnera genome evolves rapidly, making it the perfect tool for resolving ambiguities in aphid taxonomy. This study also highlights the usefulness of species delimitation methods in cospeciation studies involving species difficult to conceptualize—as is the case for bacteria—and in cases in which the taxonomy of the interacting organisms has not been determined independently and species definition depends on host association.

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Rhizobial plasmids — replication, structure and biological role

Open Life Sciences ◽

10.2478/s11535-012-0058-8 ◽

2012 ◽

Vol 7 (4) ◽

pp. 571-586 ◽

Cited By ~ 8

Author(s):

Andrzej Mazur ◽

Piotr Koper

Keyword(s):

Genome Organization ◽

Soil Bacteria ◽

Evolutionary History ◽

Bacterial Genome ◽

Biological Role ◽

Genome Architecture ◽

Genomic Knowledge ◽

History Of ◽

Cryptic Plasmids ◽

Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

10.1101/288530 ◽

2018 ◽

Author(s):

Mónica Lopes-Marques ◽

André M. Machado ◽

Raquel Ruivo ◽

Elza Fonseca ◽

Estela Carvalho ◽

...

Keyword(s):

Gene Family ◽

Metabolic Pathways ◽

Evolutionary History ◽

Gene Families ◽

Gene Repertoire ◽

Physiological Processes ◽

Complex Lipid ◽

History Of ◽

Enzyme Families ◽

Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

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Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0803654105 ◽

2008 ◽

Vol 105 (41) ◽

pp. 15961-15966 ◽

Cited By ~ 100

Author(s):

M. Brochet ◽

C. Rusniok ◽

E. Couve ◽

S. Dramsi ◽

C. Poyart ◽

...

Keyword(s):

Streptococcus Agalactiae ◽

Evolutionary History ◽

Bacterial Genome ◽

History Of

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Human Origin for Livestock-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽

10.1128/mbio.00082-12 ◽

2012 ◽

Vol 3 (2) ◽

Cited By ~ 28

Author(s):

J. Ross Fitzgerald

Keyword(s):

Staphylococcus Aureus ◽

Evolutionary History ◽

Methicillin Resistant Staphylococcus Aureus ◽

Agricultural Practices ◽

Methicillin Resistant ◽

Content Type ◽

Zoonotic Infections ◽

Ancestral Origin ◽

Important Study ◽

History Of

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of human morbidity and mortality worldwide. The emergence in the last decade of a livestock-associated MRSA (LA-MRSA) clone which also has the capacity to cause zoonotic infections in humans has raised important questions regarding its origin and its potential to cause human epidemics. An important study by L. B. Price et al. [mBio 3(1):e00305-11, 2012] provides evidence for a human ancestral origin for LA-MRSA, raising concerns about agricultural practices that may have contributed to its emergence and expansion. The study highlights the potential for comparative whole-genome sequencing of closely related strains to provide valuable insights into the evolutionary history of bacterial pathogens.

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Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131

mSphere ◽

10.1128/msphere.00121-16 ◽

2016 ◽

Vol 1 (4) ◽

Cited By ~ 42

Author(s):

Timothy J. Johnson ◽

Jessica L. Danzeisen ◽

Bonnie Youmans ◽

Kyle Case ◽

Katharine Llop ◽

...

Keyword(s):

Escherichia Coli ◽

Real Time ◽

Single Molecule ◽

Convergent Evolution ◽

Evolutionary History ◽

Gene Clusters ◽

Content Type ◽

E Coli ◽

History Of ◽

Evolutionary Success

ABSTRACT A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success. The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B− plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B− plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success.

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The past, present and future of ancient bacterial DNA

Microbial Genomics ◽

10.1099/mgen.0.000384 ◽

2020 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Nicolas Arning ◽

Daniel J. Wilson

Keyword(s):

Demographic Transition ◽

Dental Plaque ◽

Evolutionary History ◽

High Throughput Sequencing ◽

Industrial Revolution ◽

Environmental Isolates ◽

Bacterial Dna ◽

Content Type ◽

The Past ◽

History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

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Evolution of a chordate-specific mechanism for myoblast fusion

10.1101/2021.07.24.453587 ◽

2021 ◽

Author(s):

Haifeng Zhang ◽

Renjie Shang ◽

Kwantae Kim ◽

Wei Zheng ◽

Christopher J. Johnson ◽

...

Keyword(s):

Evolutionary History ◽

De Novo ◽

Myoblast Fusion ◽

Last Common Ancestor ◽

Functional Tests ◽

Evolutionary Origins ◽

New Genes ◽

History Of ◽

Early Vertebrates ◽

And Function

The size of an animal is determined by the size of its musculoskeletal system. Myoblast fusion is an innovative mechanism that allows for multinucleated muscle fibers to compound the size and strength of individual mononucleated cells. However, the evolutionary history of the control mechanism underlying this important process is currently unknown. The phylum Chordata hosts closely related groups that span distinct myoblast fusion states: no fusion in cephalochordates, restricted fusion and multinucleation in tunicates, and extensive, obligatory fusion in vertebrates. To elucidate how these differences may have evolved, we studied the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed an unexpectedly complex evolutionary history of myoblast fusion in chordates. A pre-vertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Thus, our findings reveal the evolutionary origins of chordate-specific fusogens and illustrate how new genes can shape the emergence of novel morphogenetic traits and mechanisms.

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Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

Journal of Clinical Microbiology ◽

10.1128/jcm.02198-20 ◽

2020 ◽

Vol 59 (1) ◽

pp. e02198-20

Author(s):

N. Effelsberg ◽

M. Stegger ◽

L. Peitzmann ◽

O. Altinok ◽

G. W. Coombs ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Evolutionary History ◽

De Novo ◽

Clinical Symptoms ◽

Phylogenetic Analyses ◽

Invasive Disease ◽

Phylogenetic Groups ◽

Content Type ◽

Global Epidemiology ◽

History Of

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.

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Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus

Applied and Environmental Microbiology ◽

10.1128/aem.02153-18 ◽

2018 ◽

Vol 85 (2) ◽

Cited By ~ 2

Author(s):

Liangzhi Li ◽

Zhenghua Liu ◽

Delong Meng ◽

Xueduan Liu ◽

Xing Li ◽

...

Keyword(s):

Gene Duplication ◽

Resistance Genes ◽

Evolutionary History ◽

Genomic Analysis ◽

Purifying Selection ◽

Metal Resistance ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Content Type ◽

History Of

ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

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