Redefining the invertebrate RNA virosphere : Nature : Nature Research

"Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution."



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Study adds to evidence that viruses are alive -- ScienceDaily

GEN | News Highlights:Microorganisms Slipped Genes into Humans, Primates, and Other Animals

Not all of our genetic endowment has been passed down vertically, through ancestral lines. Some of it has been acquired horizontally, from “foreign” sources, such as bacteria, protists, and fungi. The degree to which animals and humans have acquired foreign genes is unclear. It is a matter of some controversy. Yet, according to scientists from the University of Cambridge, foreign genes may have been acquired in sufficient number to influence the course of our evolution.

The transfer of genes between organisms living in the same environment is known as horizontal gene transfer (HGT). It is well known in single-celled organisms, and it is thought to be an important process that explains how quickly bacteria evolve, for example, resistance to antibiotics. In multicellular organisms, however, few cases of HGT have been documented.

HGT is thought to play an important role in the evolution of some animals, including nematode worms, which have acquired genes from microorganisms and plants, and some beetles that gained bacterial genes to produce enzymes for digesting coffee berries. However, the idea that HGT occurs in more complex animals, such as humans, rather than them solely gaining genes directly from ancestors, has been widely debated and contested.

Hoping to clarify matters, the University of Cambridge scientists took advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies, and 4 nematodes) and a simplified analysis in a further 14 vertebrates. After carrying out genome-wide comparative and phylogenetic analyses, the scientists determined that HGT in animals typically gives rise to tens or hundreds of active foreign genes, largely concerned with metabolism.

These findings appeared March 13 in the journal Genome Biology, in an article entitled, “Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.” This article confirmed that a number of genes, including the ABO blood group gene, had been acquired by vertebrates through HGT. The majority of the other genes were related to enzymes involved in metabolism.

For example, some of the genes that had been acquired by humans via horizontal transfer were shown to be involved in lipid metabolism, including the breakdown of fatty acids and the formation of glycolipids. Others were shown to be involved in immune responses, including the inflammatory response, immune cell signaling, and antimicrobial responses, while further gene categories include amino-acid metabolism, protein modification, and antioxidant activities.

The study’s lead author Alastair Crisp, D.Phil., said, "This is the first study to show how widely HGT occurs in animals, including humans, giving rise to tens or hundreds of active foreign genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution."

In humans, the scientists confirmed 17 previously reported genes acquired from HGT, and identified 128 additional foreign genes in the human genome that have not previously been reported.

A Movable Defense: The virome and our genomes| The Scientist Magazine®

Researchers now recognize that genetic material, once simplified into neat organismal packages, is not limited to individuals or even species. Viruses that pack genetic material into stable infectious particles can incorporate some or all of their genes into their hosts’ genomes, allowing remnants of infection to remain even after the viruses themselves have moved on. On a smaller scale, naked genetic elements such as bacterial plasmids and transposons, or jumping genes, often shuttle around and between genomes. It seems that the entire history of life is an incessant game of tug-of-war between such mobile genetic elements (MGEs) and their cellular hosts.

MGEs pervade the biosphere. In all studied habitats, from the oceans to soil to the human intestine, the number of detectable virus particles, primarily bacteriophages, exceeds the number of cells at least tenfold, and maybe much more. Furthermore, MGEs and their remnants constitute large portions of many organisms’ genomes—as much as two-thirds of the human genome and up to 90 percent in plants such as corn.

Horizontal genome transfer as an asexual path to the formation of new species : Nature : Nature Publishing Group

Allopolyploidization, the combination of the genomes from two different
species, has been a major source of evolutionary innovation and a driver
of speciation and environmental adaptation.
In plants, it has also contributed greatly to crop domestication, as
the superior properties of many modern crop plants were conferred by
ancient allopolyploidization events.
It is generally thought that allopolyploidization occurred through
hybridization events between species, accompanied or followed by genome
duplication.
Although many allopolyploids arose from closely related species
(congeners), there are also allopolyploid species that were formed from
more distantly related progenitor species belonging to different genera
or even different tribes.
Here we have examined the possibility that allopolyploidization can
also occur by asexual mechanisms. We show that upon grafting—a mechanism
of plant–plant interaction that is widespread in nature—entire nuclear
genomes can be transferred between plant cells. We provide direct
evidence for this process resulting in speciation by creating a new
allopolyploid plant species from a herbaceous species and a woody
species in the nightshade family. The new species is fertile and
produces fertile progeny. Our data highlight natural grafting as a
potential asexual mechanism of speciation and also provide a method for
the generation of novel allopolyploid crop species.

Bacteria recycle broken DNA: Modern bacteria can add DNA from creatures long-dead to its own

 "From a bacteria’s perspective the environment is one big DNA waste yard. Researchers have now shown that bacteria can take up small as well as large pieces of old DNA from this scrapheap and include it in their own genome. This discovery may have major consequences – both in connection with resistance to antibiotics in hospitals and in our perception of the evolution of life itself."

PLOS Genetics: A Review of Bacteria-Animal Lateral Gene Transfer May Inform Our Understanding of Diseases like Cancer

 Interesting conclusions:

Extensive lateral gene transfer (LGT)  has been detected between bacteria and animals, particularly between endosymbionts and their hosts. Recent LGT may be associated specifically with endosymbionts that colonize germ cells and the germ stem cell of their respective hosts. The extensive LGT observed between Wolbachia endosymbionts and their invertebrate hosts suggests that LGT involving bacteria and animals may occur more frequently than was thought a decade ago. While vertebrates have an immune system and segregated gametes that may prevent transfers like those seen in invertebrates, transfers to the vertebrate somatic genome have not been appreciated and warrant further examination. Bacterial DNA integration may be a mutagen associated with noninherited genetic diseases, like cancer, as described in a recent paper demonstrating LGT from Acinetobacter spp. in leukemia samples and from Pseudomonas spp. in stomach cancer samples.

Viruses (other than retroviruses) also appear to have been integrated into animal genomes 
See :- 

Endogenous viral elements in animal genomes Katsourakis and Gifford, 2010  

Bacteriophages shuttle genes between diverse ecosystems.: Going Viral | The Scientist Magazine®

 "As little more than carriers of DNA, bacteriophages serve to shuttle genes between diverse ecosystems. The viruses take up genetic material from their bacterial hosts and donate it to future hosts, both near and far. Such genetic movement can spread bacterial traits such as virulence, antibiotic resistance, or adhesion capability—and even introduce novel genes to new environments. While viruses can only move short distances outside of a host, the migration of bacteria, or of the megafauna that bacteria infect, allows phages to traverse the globe."

Futurity.org – Surprise virus caused blue chicken eggs

A retrovirus is a virus that, unlike most cellular organisms, carries its genetic blueprint in the form of ribonucleic acid (RNA). It reproduces itself in a host cell using a special enzyme called “reverse transcriptase” which transcribes RNA into deoxyribonucleic acid (DNA).
This makes it possible for genetic material from a retrovirus to become permanently incorporated into the DNA of an infected cell. In this case, the retrovirus’ effect was to trigger an accumulation of a green-blue bile pigment called biliverdin in the eggshell as the egg develops in the hen.
“It shows the importance of viruses in shaping evolution and diversity of species

Ancient viruses that function in early human development may play role in cancer

 Up to 98 percent of human genomic matter is known as "junk" or "dark matter" non-coding DNA, and had for years attracted little interest among scientists who doubted its role in human health and disease. Recent research has begun to identify that part of that non-coding DNA is used by the cell to make RNA such as vlincRNA, highly tissue-specific RNA chains of unusually large lengths, many of which are only found in embryonic or cancerous cells. VlincRNAs found in these two types of cells tend to be expressed based upon genetic signals from ancient viruses that invaded our ancestors' genome millions of years ago and were gradually "domesticated" over evolutionary time. The number of vlincRNAs expressed by these domesticated viral sequences correlates with both embryonic development and malignant cancers.

Integrated virus-host methylome analysis in head and neck squamous cell carcinoma.

 One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DNA methylation analysis using MeDIP-seq of HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC). We determined the viral subtype to be HPV-16 in all cases and show that HPV-16 integrates into the host genome at multiple random sites and that this process predominantly involves the transcriptional repressor gene (E2) in the viral genome. Comparative analysis identified 453 (FDR ≤ 0.01) differentially methylated regions (DMRs) in the HPV+ host methylome. Bioinformatics characterization of these DMRs confirmed the previously reported cadherin genes to be affected but also revealed new targets for HPV-mediated methylation changes at regions not covered by array-based platforms, including the recently identified super-enhancers.

Bacterial DNA may integrate into human genome more readily in tumor tissue

: "Bacterial DNA may integrate into the human genome more readily in tumors than in normal human tissue, according to a new study from the University of Maryland School of Medicine's Institute for Genome Sciences. Researchers analyzed genomic sequencing data available from the Human Genome Project, the 1,000 Genomes Project and The Cancer Genome Atlas (TCGA). They considered the phenomenon of lateral gene transfer (LGT), the transmission of genetic material between organisms in the absence of sex."

DNA Jumps Between Vertebrates | The Scientist Magazine®

The lateral transfer of genetic information across species is common in bacteria, but rare among vertebrates—or so scientists believed. Now, researchers have demonstrated that a particular DNA sequence has likely jumped several times between the genomes of reptiles, marsupials, and mammals. The study was published this week (31 December) in the Proceedings of the National Academy of Sciences.

Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

Horizontal gene transfer (HGT) is largely responsible for increasing the incidence of antibiotic-resistant infections worldwide. While studies have focused on HGTin vivo, this work investigates whether the ability of pathogens to persist in the environment, particularly on touch surfaces, may also play an important role.Escherichia coli, virulent clone ST131, and Klebsiella pneumoniae harboring extended-spectrum-β-lactamase (ESBL) bla_CTX-M-15 and metallo-β-lactamasebla_NDM-1, respectively, exhibited prolonged survival on stainless steel, with approximately 10⁴ viable cells remaining from an inoculum of 10⁷ CFU per cm²after 1 month at 21°C. HGT of bla to an antibiotic-sensitive but azide-resistant recipient E. coli strain occurred on stainless steel dry touch surfaces and in suspension but not on dry copper. The conjugation frequency was approximately 10 to 50 times greater and occurred immediately, and resulting transconjugants were more stable with ESBL E. coli as the donor cell than with K. pneumoniae, butbla_NDM-1 transfer increased with time. Transconjugants also exhibited the same resistance profile as the donor, suggesting multiple gene transfer. Rapid death, inhibition of respiration, and destruction of genomic and plasmid DNA of both pathogens occurred on copper alloys accompanied by a reduction in bla copy number. Naked E. coli DNA degraded on copper at 21°C and 37°C but slowly at 4°C, suggesting a direct role for the metal. Persistence of viable pathogenic bacteria on touch surfaces may not only increase the risk of infection transmission but may also contribute to the spread of antibiotic resistance by HGT. The use of copper alloys as antimicrobial touch surfaces may help reduce infection and HGT.

IMPORTANCE Horizontal gene transfer (HGT) conferring resistance to many classes of antimicrobials has resulted in a worldwide epidemic of nosocomial and community infections caused by multidrug-resistant microorganisms, leading to suggestions that we are in effect returning to the preantibiotic era. While studies have focused on HGT in vivo, this work investigates whether the ability of pathogens to persist in the environment, particularly on touch surfaces, may also play an important role. Here we show prolonged (several-week) survival of multidrug-resistant Escherichia coli and Klebsiella pneumoniae on stainless steel surfaces. Plasmid-mediated HGT of β-lactamase genes to an azide-resistant recipient E. coli strain occurred when the donor and recipient cells were mixed together on stainless steel and in suspension but not on copper surfaces. In addition, rapid death of both antibiotic-resistant strains and destruction of plasmid and genomic DNA were observed on copper and copper alloy surfaces, which could be useful in the prevention of infection spread and gene transfer.

Blood groups act as protection against infection

(Medical Xpress)—Humans may have acquired enzymes that make blood groups from bacteria to hinder the spread of viruses in the population, suggests a study led by scientists at the University of Bath."

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Moss Harbors Foreign Genes (viral, bacterial and fungal)| The Scientist Magazine®

Land plants emerged around half a billion years ago, having evolved from green aquatic algae. Today, a representative of these early land-dwelling species—a moss—hints that genes from other kingdoms of life may have helped the ancient colonizers flourish on land.

Human and soil bacteria swap antibiotic-resistance genes

When Vaccines Turn Vicious | The Scientist

The very vaccines used to prevent a respiratory disease in chickens caused several recent outbreaks of the same disease at farms across Australia, according to a report published today (July 12) in Science. Different weakened versions of a live herpes virus used in the vaccines exchanged portions of their genomes, resulting in virulent, disease-causing strains. This suggests that such in-the-field genetic recombination is more common than previously thought, and has implications for both animal and human health.

Horizontal Gene Transfer in Microorganisms | Book

MicrobeWorld - Viruses con bacteria into working for them

These viruses are carrying genetic material taken from their previous bacterial hosts that tricks the new host into using its own machinery to activate the genes: