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PubMed1999

Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria.

Temperate Siphoviridae from an evolutionarily related branch of low GC content gram-positive bacteria share a common genetic organization of lysogeny-related genes and the predicted proteins are linked by many sequence similarities. Their compact lysogeny modules [integrase/1-2 orfs (phage exclusion? and metalloproteinase motif proteins)/cI-like repressor/cro-like repressor/antirepressor (optional)] differ clearly from that of lambda-like and L5-like viruses, the two currently established genera of temperate Siphoviridae, while they resemble those of the P2-like genus of Myoviridae. In all known temperate Siphoviridae from low GC content gram-positive bacteria the lysogeny module is flanked by the lysis module and the DNA replication module. This modular organization is again distinct from that of the known genera of temperate Siphoviridae. On the basis of comparative sequence analysis we propose a new genus of Siphoviridae: "Sfi21-like" phages. With a larger database of phage sequences it might be possible to establish a genomics-based phage taxonomy and to retrace the evolutionary history of selected phage modules or individual phage genes. The antirepressor of Sfi21-like phages has an unusual widespread distribution since proteins with high aa similarity (40%) were found not only in phages from gram-negative bacteria, but also in insect viruses.

Amino Acid Sequence↗
PubMed2000

Comparative genomics of the late gene cluster from Lactobacillus phages.

Three prophage sequences were identified in the Lactobacillus johnsoni strain NCC533. Prophage Lj965 predicted a gene map very similar to those of pac-site Streptococcus thermophilus phages over its DNA packaging and head and tail morphogenesis modules. Sequence similarity linked the putative DNA packaging and head morphogenesis genes at the protein level. Prophage Lj965/S. thermophilus phage Sfi11/Lactococcus lactis phage TP901-1 on one hand and Lactobacillus delbrueckii phage LL-H/Lactobacillus plantarum phage phig1e/Listeria monocytogenes phage A118 on the other hand defined two sublines of structural gene clusters in pac-site Siphoviridae from low-GC Gram-positive bacteria. Bacillus subtilis phage SPP1 linked both sublines. The putative major head and tail proteins from Lj965 shared weak sequence similarity with phages from Gram-negative bacteria. A clearly independent line of structural genes in Siphoviridae from low-GC Gram-positive bacteria is defined by temperate cos-site phages including Lactobacillus gasseri phage adh, which also shared sequence similarity with phage D3 infecting a Gram-negative bacterium. A phylogenetic tree analysis demonstrated that the ClpP-like protein identified in four cos-site Siphoviridae from Lactobacillus, Lactococcus, Streptococcus, and Pseudomonas showed graded sequence relationships. The tree suggested that the ClpP-like proteins from the phages were not acquired by horizontal gene transfer from their corresponding bacterial hosts.

Amino Acid Sequence↗
PubMed2001

Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates.

The HERV-H family is one of the largest human endogenous retrovirus families, with approximately 1000 elements. Using a direct coupled in vitro transcription/translation approach (PTT for protein truncation test) and an extended series of primers on human genomic DNA, on monochromosomal hybrids and on a BAC library, we could demonstrate that there are only three envelopes with a large open reading frame encompassing the immunosuppressive (ISU) domain, corresponding to 62-, 60-, and 59-kDa potential translational products. The associated proviruses, HERV-H/env62, HERV-H/env60, and HERV-H/env59 were sequenced together with their flanking DNA and mapped by FISH, and their entry times within the primate lineage were determined. Analysis of the LTR sequences revealed numerous recombinational and/or homogenization events in the course of evolution, with divergences between 5' and 3' LTRs higher than expected for a simple time-dependent genetic drift. PTT analyses further revealed that the three large envelopes in humans are prematurely stopped in the majority of primates, and sequencing of the largest envelope gene, from HERV-H/env62, in five human individuals revealed two polymorphic sites. The results are consistent with the absence of a strong selective pressure for the conservation of a functional envelope gene of possible benefit for the host, but do not exclude somatic effects possibly associated with the immunosuppressive domain carried by these genes.

Animals↗
PubMed2001

Molecular characterization of the genome of Maize rayado fino virus, the type member of the genus Marafivirus.

The complete nucleotide sequence of the single-stranded RNA genome of Maize rayado fino virus (MRFV), the type member of the genus Marafivirus, is 6305 nucleotides (nts) in length and contains two putative open reading frames (ORFs). The largest ORF (nt 97-6180) encodes a polyprotein of 224 kDa with sequence similarities at its N-terminus to the replication-associated proteins of other viruses with positive-strand RNA genomes and to the papainlike protease domain found in tymoviruses. The C-terminus of the 224-kDa ORF also encodes the MRFV capsid protein. A smaller, overlapping ORF (nt 302-1561) encodes a putative protein of 43 kDa with unknown function but with limited sequence similarities to putative movement proteins of tymoviruses. The nucleotide sequence and proposed genome expression strategy of MRFV is most closely related to that of oat blue dwarf virus (OBDV). Unlike OBDV, MRFV RNA does not appear to contain a poly(A) tail, and it encodes a putative second overlapping open reading frame.

Amino Acid Sequence↗
PubMed2001

Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: evolution, structure, and genome organization of lactococcal bacteriophages.

A complete analysis of the entire genome of the temperate lactococcal bacteriophage TP901-1 has been performed and the function of 21 of 56 TP901-1-encoded ORFs has been assigned. This knowledge has been used to propose 10 functional modules each responsible for specific functions during bacteriophage TP901-1 proliferation. Short regions of microhomology in intergenic regions present in several lactococcal bacteriophages and chromosomal fragments of Lactococcus lactis are suggested to be points of exchange of genetic material through homologous recombination. Our results indicate that TP901-1 may have evolved by homologous recombination between the host chromosome and a mother phage and support the observation that phage remnants as well as prophages located in the Lactococcus chromosome contribute significantly to bacteriophage evolution. Some proteins encoded in the early transcribed region of the TP901-1 genome were more homologous to proteins encoded by phages infecting gram-positive hosts other than L. lactis. This protein homology argues for the occurrence of horizontal genetic exchange among these bacteriophages and indicates that they have access to a common gene pool.

Bacteriophages↗
PubMed2001

Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions.

The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment. Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the replisome organizer gene that may prevent the induction of the prophage. The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205 extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations: one in the replisome organizer gene and another in the gene encoding the portal protein. Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence factors: prophage-encoded toxins acting as superantigens that may contribute to the immune deregulation observed during invasive streptococcal infections. The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. The genes were nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer. The trend for prophage genome inactivation was even more evident for the remaining five prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria and suggest elements of genetic cooperation and elements of an arms race in this host-parasite relationship.

Bacteriophages↗
PubMed2006

Transitions in understanding of RNA viruses: a historical perspective.

This chapter documents that RNA viruses have been known for over a century to be genetically variable. In recent decades, genetic and molecular analyses demonstrate that they form RNA quasispecies populations; the most rapidly mutating, highly variable and genetically versatile life forms on earth. Their enormous populations, rapid replication and extreme genetic plasticity can allow rates of evolution that exceed those of their eukaryotic host populations by millions-fold.

Evolution, Molecular↗
PubMed2005

Australian bat lyssavirus: a recently discovered new rhabdovirus.

Australian bat lyssavirus (ABLV), first identified in 1996, has been associated with two human fatalities. ABLV is genetically and serologically distinct from, but is closely related to, classical rabies. It has a bullet-shaped morphology by electron microscopy. There are two strains of ABLV known: one circulates in frugivorous bats, sub-order Megachiroptera, and the other circulates in the smaller, mainly insectivorous bats, sub-order Microchiroptera. Each strain has been associated with one human fatality. Surveillance indicates infected bats are widespread at a low frequency on the Australian mainland. It is unclear how long ABLV has been present in Australia, although molecular clock studies suggest the two strains separated 950 or 1,700 years ago based on synonymous or non-synonymous nucleotide changes, respectively. Recent serological surveys suggest a closely related virus may exist in the Philippines. Due to demonstrated cross-protection in mice, rabies vaccine is used to prevent infection. Rabies post-exposure prophylaxis (PEP) protocols have been adopted for when a human is scratched or bitten by a suspect bat. A long-term commitment to public health programs that test bats that have been involved in scratch or bite incidents, followed by PEP if appropriate, will be necessary to minimise further human infection.

Animals↗
PubMed2025

An Evolutionary Framework Exploiting Virologs and Their Host Origins to Inform Poxvirus Protein Functions.

Poxviruses represent evolutionary successful infectious agents. As a family, poxviruses can infect a wide variety of species including humans, fish, and insects. While many other viruses are species-specific, an individual poxvirus species is often capable of infecting diverse hosts and cell types. For example, the prototypical poxvirus, vaccinia, is well known to infect numerous human cell types but can also infect cells from divergent hosts like frog neurons. Notably, poxvirus infections result in both detrimental human and animal diseases. The most infamous disease linked to a poxvirus is smallpox caused by variola virus. Poxviruses are large double-stranded DNA viruses, which uniquely replicate in the cytoplasm of cells. The model poxvirus genome encodes ~200 nonoverlapping protein-coding open reading frames (ORFs). Poxvirus gene products impact various biological processes like the production of virus particles, the host range of infectivity, and disease pathogenesis. In addition, poxviruses and their gene products have biomedical application with several species commonly engineered for use as vaccines and oncolytic virotherapy. Nevertheless, we still have an incomplete understanding of the functions associated with many poxvirus genes. In this chapter, we outline evolutionary insights that can complement ongoing studies of poxvirus gene functions and biology, which may serve to elucidate new molecular activities linked to this biomedically relevant class of viruses.

Animals↗
PubMed2001

Host mediated variation and receptor binding specificity of influenza viruses.

There are at least two possible mechanisms for the host range variation of influenza A viruses. First mechanism is the pressure of the antibody, this results has already reported by us, in 1989(12). In this case, Ser 205 which is located in antigenic site D in the hemagglutinin trimer. When Ser 205 is substituted to Tyr, receptor binding specificity become 2-6 predominant rather than 2-3 predominant. Ser205 is located far away from the receptor binding pocket in the subunit itself, however, very close to the pocket in the next subunit. When the Ser 205 is substituted to bulky amino acid Tyr, the three dimensional structure of the receptor binding pocket in next subunit may be influenced to become 2-6 binding property rather than 2-3 binding. Second mechanism is the selective pressure for the appearance of host cell variant with altered receptor binding specificities. In this case, amino acid 226 located in receptor binding pocket is clitical for the recognition of 2-6 and 2-3 linkages. Only single amino acid alteration of Leu 226 to Gln made remarkable change of receptor binding specificity 2-6 to 2-3. In this study, we also identified amino acid 155 Thr, 158 Glu, and 228 Ser of the hemagglutinin which may be clitical for the recognition of the molecular species of sialic acid, such as Neu5Ac and Neu5Gc. Very recently, we reported the amino acid residues contributing to the substrate specificity of the influenza A virus sialidase. If these amino acid alteration occurres in the host animal bodies in nature, the virus aquires the new receptor binding specificity which allows the infection to the different animal species, such as bird to human population. This process may be one of the important mechanism for the host mediated variation, and the influenza virus transmission between different hosts, and also emerging of new subtypes of influenza viruses in human population.

Animals↗
PubMed2003

Molecular evolution of adenoviruses.

New advances in the field of genetic characterization of adenoviruses originating from different animal species are summarized. Variations seen in the host range and specificity, pathogenicity, genomic arrangement or gene complement are much wider than expected based on previous studies of human adenoviruses. Several exceptional adenoviruses from the two traditional conventional genera are now removed, and proposed to form at least two new genera. The eventual host origin of the new genera, however, is not clarified. Novel results from the genomic and phylogenetic analyses of adenoviruses originating from lower vertebrate species (including reptiles, amphibians and fish) seem to imply that probably five major clusters of adenoviruses exist corresponding to the five major classes of Vertebrata. Adenoviruses, which are now suspected to have common origin with enterobacterium phages from the family Tectiviridae, are perhaps very ancient indeed, and may have undergone a co-evolution with vertebrate hosts.

Adenoviridae↗
PubMed1993

Molecular biology and evolution of filoviruses.

The family Filoviridae contains extremely pathogenic human viruses causing a fulminating, febrile hemorrhagic disease. Filoviruses are enveloped, filamentous particles with a nonsegmented negative-strand RNA genome showing the gene arrangement 3'-NP-VP35-VP40-GP-VP30-VP24-L-5'. Genes are flanked by highly conserved transcriptional signals and are generally separated by variable intergenic regions. They are transcribed into monocistronic polyadenylated messenger RNAs which contain relatively long 5' and 3' untranslated regions. Seven structural proteins are encoded by the genome of which four form the helical nucleocapsid (NP-VP35-VP30-L), two are membrane-associated (VP40-VP24), and one is a transmembrane glycoprotein (GP). Comparison of filovirus genomes with those of other nonsegmented negative-strand RNA viruses suggest comparable mechanisms of transcription and replication and a common evolutionary lineage for all these viruses. Sequence analyses of single genes, however, showed that filoviruses are more closely related to paramyxoviruses, particularly human respiratory syncytial virus. These data support the concept of the taxonomic order Mononegavirales for all nonsegmented negative-strand RNA viruses and the classification of Marburg virus, Ebola virus, and Reston virus in the family Filoviridae, separate from the families Paramyxoviridae and Rhabdoviridae.

Animals↗
PubMed1990

Evolution of the NS genes of the influenza A viruses. I. The genetic relatedness of the NS genes of animal influenza viruses.

We compared the nucleotide sequences of the NS genes of 13 animal influenza viruses belonging to human, swine, avian, and equine viruses for the study of the genetic relatedness of the NS genes in animal influenza viruses. The NS genes of three virus strains A/chicken/Brescia/02, A/equine/Prague/56, and A/equine/Miami/63 were newly sequenced. The base sequence homologies between the NS genes of avian, human, swine, and the A/equine/Miami/63 viruses were 87.8% or higher. On the other hand, the base sequence of the NS gene of the A/equine/Prague/56 virus differed widely from those of other viruses analyzed in the present study. We constructed a model of the genetic tree of the NS genes of avian and equine influenza viruses by a modified Farris method. For comparison of the NS genes between human and avian viruses, we estimated the speed of the nucleotide substitutions of the avian influenza NS genes. It was roughly constant, even though the substitutions did not occur sequentially. The nucleotide substitution rate of the NS genes of avian influenza viruses was one-third to one-fourth that of human influenza viruses. We deduced the time of separation between the NS genes of human and avian influenza viruses during evolution.

Animals↗
PubMed1995

Origin and evolution of viroids and viroid-like satellite RNAs.

Viroids, the smallest and simplest agents of infectious disease, cause a number of economically important diseases of crop plants. Present evidence indicates that most of these diseases originated recently (in the 20th century) by chance transfer of viroids from endemically infected wild plants or by use of viroid-infected germplasm during plant breeding. Modern agricultural practices, such as widespread monoculture of genetically identical plants, and worldwide distribution of planting material, has made it possible for the pathogens to maintain themselves in the crop plants and to conquer new territories. Phylogenetic analysis of their nucleotide sequences indicates that viroids and satellite RNAs represent a monophyletic group, with all but the two self-cleaving viroids forming one cluster and the satellite RNAs another. The two self-cleaving viroids are phylogenetically distant from either cluster; they may represent ancestral forms. Results from site-directed mutagenesis experiments indicate that, upon exposure to selective pressures, viroids can evolve extremely rapidly, with another, fitter, component of the quasi-species often becoming dominant within days or weeks. This extreme plasticity of their nucleotide sequences establishes viroids as the most rapidly evolving biological system known.

Base Sequence↗