How viruses made us humans

The Oxford Handbook of Human Symbolic Evolution ◽

10.1093/oxfordhb/9780198813781.013.5 ◽

2021 ◽

Author(s):

Guenther Witzany

Keyword(s):

Social Life ◽

Visual Information ◽

Viral Infections ◽

Genetic Material ◽

Mobile Genetic Elements ◽

Genetic Regulatory Networks ◽

Social Recognition ◽

Endogenous Retroviruses ◽

Evolutionary Novelty ◽

Genetic Elements

Current research on the origin of DNA and RNA, viruses, and mobile genetic elements prompts a re-evaluation of the origin and nature of genetic material as the driving force behind evolutionary novelty. While scholars used to think that novel features resulted from random genetic mutations of an individual’s specific genome, today we recognize the important role that acquired viruses and mobile genetic elements have played in introducing evolutionary novelty within the genomes of species. Viral infections and subviral RNAs can enter the host genome and persist as genetic regulatory networks. Persistent viral infections are also important to understand the split between great apes and humans. Nearly all mammals and nonhuman primates rely on olfaction, i.e., chemoreception as the basis of the sense of smell for social recognition, group membership, and the coordination of organized social life. Humans, however, evolved other means to establish social bonding, because several infection waves by endogenous retroviruses caused a loss of odor receptors in human ancestors. The human independence from olfaction for social recognition was in turn one driver of the rather abrupt human transition to dependence on visual information, gesture production, and facial recognition that are at the roots of language-based communication.

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Streptococcus zooepidemicus and Streptococcus equi evolution: the role of CRISPRs

Biochemical Society Transactions ◽

10.1042/bst20130165 ◽

2013 ◽

Vol 41 (6) ◽

pp. 1437-1443 ◽

Cited By ~ 9

Author(s):

Andrew S. Waller ◽

Carl Robinson

Keyword(s):

Genome Stability ◽

Genetic Material ◽

Economic Cost ◽

Opportunistic Pathogen ◽

Mobile Genetic Elements ◽

Limited Range ◽

Gene Gain ◽

Streptococcus Zooepidemicus ◽

Genetic Elements ◽

Streptococcus Equi

The host-restricted bacterium Streptococcus equi is the causative agent of equine strangles, the most frequently diagnosed infectious disease of horses worldwide. The disease is characterized by abscessation of the lymph nodes of the head and neck, leading to significant welfare and economic cost. S. equi is believed to have evolved from an ancestral strain of Streptococcus zooepidemicus, an opportunistic pathogen of horses and other animals. Comparison of the genome of S. equi strain 4047 with those of S. zooepidemicus identified examples of gene loss due to mutation and deletion, and gene gain through the acquisition of mobile genetic elements that have probably shaped the pathogenic specialization of S. equi. In particular, deletion of the CRISPR (clustered regularly interspaced short palindromic repeats) locus in the ancestor of S. equi may have predisposed the bacterium to acquire and incorporate new genetic material into its genome. These include four prophages and a novel integrative conjugative element. The virulence cargo carried by these mobile genetic elements is believed to have shaped the ability of S. equi to cause strangles. Further sequencing of S. zooepidemicus has highlighted the diversity of this opportunistic pathogen. Again, CRISPRs are postulated to influence evolution, balancing the need for gene gain over genome stability. Analysis of spacer sequences suggest that these pathogens may be susceptible to a limited range of phages and provide further evidence of cross-species exchange of genetic material among Streptococcus pyogenes, Streptococcus agalactiae and Streptococcus dysgalactiae.

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Dynamics between horizontal gene transfer and acquired antibiotic resistance in S. Heidelberg following in vitro incubation in broiler ceca

10.1101/684787 ◽

2019 ◽

Author(s):

Adelumola Oladeinde ◽

Kimberly Cook ◽

Steven M. Lakin ◽

Zaid Abdo ◽

Torey Looft ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gastrointestinal Tract ◽

Gut Microbiome ◽

Genetic Material ◽

Mobile Genetic Elements ◽

Important Food ◽

Genetic Elements ◽

Food Borne ◽

Acquired Antibiotic Resistance

AbstractThe chicken gastrointestinal tract harbors taxa of microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from ceca flora to Salmonella enterica serovar Heidelberg (S. Heidelberg). We used whole genome sequencing and resistome enrichment to decipher the interactions between S. Heidelberg, gut microbiome and acquired antibiotic resistance. After 48 h incubation of ceca under microaerophilic conditions, one S. Heidelberg isolate was recovered with an acquired Inck2 plasmid (88 kb) encoding extended β-lactamase producing gene (blaCMY-2). In vitro, this plasmid was transferrable between E. coli and S. Heidelberg strains, but transfer was unsuccessful between S. Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of the dynamics between an important food-borne pathogen and the chicken gut microbiome.ImportanceS. Heidelberg is a clinically important serovar, linked to food-borne illness and among the top 5 serovars isolated from poultry in USA and Canada. Acquisition of new genetic material from microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding on the dynamic interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this study, we show that the native flora in the broiler ceca were capable of transferring mobile genetic elements carrying AmpC β-lactamase (blaCMY-2) gene to an important food-borne pathogen S. Heidelberg. The potential role for P1-like bacteriophage transduction was also discussed.

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MECHANISMS OF RESISTANCE TRANSFER IN BACTERIA

Archives of Veterinary Medicine ◽

10.46784/e-avm.v3i1.195 ◽

2010 ◽

Vol 3 (1) ◽

pp. 85-92 ◽

Cited By ~ 1

Author(s):

Maja Velhner ◽

Jelena Petrović ◽

Igor Stojanov ◽

Radomir Ratajac ◽

Dragica Stojanović

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Genomic Structure ◽

Genetic Material ◽

Mobile Genetic Elements ◽

Mechanisms Of Resistance ◽

Genetic Elements ◽

Resistance Transfer ◽

The Future ◽

Microbial Infections

Wide application of antimicorbial agents forces bacteria to utilize specific genes and rearrange genomic structure in order to survive in the environment. In this article lateral gene transfer, mobile genetic elements, plasmid mediated resistance and spontaneous mutators in bacteria are briefly described. This resourceful means, by which microorganisms manage to communicate and transfer genetic material in their own kingdom, raises concerns about the possibility to keep microbial infections under control in the future.

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CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

10.1101/2021.04.12.439454 ◽

2021 ◽

Author(s):

Elizabeth Pursey ◽

Tatiana Dimitriu ◽

Fernanda L. Paganelli ◽

Edze R. Westra ◽

Stineke van Houte

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Genes ◽

Bacterial Pathogens ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Defence System

AbstractThe acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential “immunocompromised” state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.

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Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements

Viruses ◽

10.3390/v11111003 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1003 ◽

Cited By ~ 5

Author(s):

Terje Dokland

Keyword(s):

High Frequency ◽

Genetic Material ◽

Low Frequency ◽

Mobile Genetic Elements ◽

Chromosomal Dna ◽

Genetic Elements ◽

Assembly Pathway ◽

Phage Assembly ◽

Phage Production ◽

Generalized Transduction

Horizontal transfer of mobile genetic elements (MGEs) is a key aspect of the evolution of bacterial pathogens. Transduction by bacteriophages is especially important in this process. Bacteriophages—which assemble a machinery for efficient encapsidation and transfer of genetic material—often transfer MGEs and other chromosomal DNA in a more-or-less nonspecific low-frequency process known as generalized transduction. However, some MGEs have evolved highly specific mechanisms to take advantage of bacteriophages for their own propagation and high-frequency transfer while strongly interfering with phage production—“molecular piracy”. These mechanisms include the ability to sense the presence of a phage entering lytic growth, specific recognition and packaging of MGE genomes into phage capsids, and the redirection of the phage assembly pathway to form capsids with a size more appropriate for the size of the MGE. This review focuses on the process of assembly redirection, which has evolved convergently in many different MGEs from across the bacterial universe. The diverse mechanisms that exist suggest that size redirection is an evolutionarily advantageous strategy for many MGEs.

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CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0464 ◽

2021 ◽

Vol 377 (1842) ◽

Author(s):

Elizabeth Pursey ◽

Tatiana Dimitriu ◽

Fernanda L. Paganelli ◽

Edze R. Westra ◽

Stineke van Houte

Keyword(s):

Antibiotic Resistance ◽

System Analysis ◽

Bacterial Pathogens ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Multidrug Resistant ◽

Human Pathogens ◽

Genetic Elements ◽

Defence System

The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus , Staphylococcus , Acinetobacter and Pseudomonas . We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential ‘immunocompromised’ state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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