A proviral puzzle with a prosimian twist

Johnson, Welkin E.

doi:10.1073/pnas.0811419106

Cited by 6 publications

(5 citation statements)

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“…Virus gene rearrangements participate and underlie the process of generation of new structures, metabolic ways and gene regulation that result in evolutionary changes (Casjens, 2003;Feschotte & Gilbert, 2012;Johnson, 2008;Johnson & Coffin, 1999;Tristem, 2000). For instance, the action and expression of a gene derived from an endogenous retrovirus participates in the formation of placenta in mammals (Mallet et al, 2004).…”

Section: Virus and Bacteria: Building The Netmentioning

confidence: 99%

Microbiome, holobiont and the net of life

Salvucci

2014

Critical Reviews in Microbiology

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Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.

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Section: Virus and Bacteria: Building The Netmentioning

confidence: 99%

Microbiome, holobiont and the net of life

Salvucci

2014

Critical Reviews in Microbiology

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“…They are the cause of a variety of chronic diseases and constitute a major public health concern, especially due to the HIV/AIDS pandemic. In contrast to other retroviral genera, lentiviruses rarely generate ERV copies [ 1 ]. The ERVs are formed following germline infection and further vertical transmission of the integrated provirus [ 2 ].…”

Section: Resultsmentioning

confidence: 99%

“…The ERVs are formed following germline infection and further vertical transmission of the integrated provirus [ 2 ]. The presence of such genomic “viral fossils” enables the study of long-term evolutionary history and evolution of lentiviruses [ 1 ]. The first endogenous lentivirus has been described in 2007 in the genome of European rabbit [ 3 ].…”

Section: Resultsmentioning

confidence: 99%

Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates

et al. 2014

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BackgroundA significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes.FindingsUsing the in silico strategy, we have screened 104 publicly available vertebrate genomes for the presence of endogenous lentivirus sequences. In addition to the previously described cases, the search revealed the presence of endogenous lentivirus in the genome of Malayan colugo (Galeopterus variegatus). At least three complete copies of this virus, denoted ELVgv, were detected in the colugo genome, and approximately one hundred solo LTR sequences. The assembled consensus sequence of ELVgv had typical lentivirus genome organization including three predicted accessory genes. Phylogenetic analysis placed this virus as a distinct subgroup within the lentivirus genus. The time of insertion into the dermopteran lineage was estimated to be more than thirteen million years ago.ConclusionsWe report the discovery of the first endogenous lentivirus in the mammalian order Dermoptera, which is a taxon close to the Primates. Lentiviruses have infiltrated the mammalian germline several times across millions of years. The colugo virus described here represents possibly the oldest documented endogenization event and its discovery can lead to new insights into lentivirus evolution. This is also the first report of an endogenous lentivirus in an Asian mammal, indicating a long-term presence of this retrovirus family in Asian continent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-014-0084-x) contains supplementary material, which is available to authorized users.

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“…The continuing sequenciation of phages and virus is a way to the unknown (Rosario et al, 2009 ). Continued virus gene rearrangements derived from virus particles have formed a mosaic gene that underlies the creation of new structures and the generation of new species (Tristem et al, 1995 ; Johnson and Coffin, 1999 ; Tristem, 2000 ; Casjens, 2003 ; Johnson, 2008 ).…”

Section: Other Perspectivesmentioning

confidence: 99%

Selfishness, warfare, and economics; or integration, cooperation, and biology

Salvucci¹

2012

Front. Cell. Inf. Microbio.

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The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an “infective” way and become an essential part of multicellular organisms. They have content with “biological sense” i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a “superorganism”) along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.

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A proviral puzzle with a prosimian twist

Cited by 6 publications

References 9 publications

Microbiome, holobiont and the net of life

Microbiome, holobiont and the net of life

Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates

Selfishness, warfare, and economics; or integration, cooperation, and biology

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