Asteroid strikes get all the coverage, but “Medea Hypothesis” author Peter Ward argues that most of Earth’s mass extinctions were caused by lowly bacteria. The culprit, a poison called hydrogen sulfide, may have an interesting application in medicine.
The acquisition of foreign DNA is a fundamental process in the diversification and adaptation of most bacterial species. Horizontal transfer of plasmids, bacteriophages, transposons, integrons, conjugative transposons, integrative conjugative elements (ICEs) and genomic islands is of particular importance to many plant and human pathogens. These integrative elements can encode functions that increase bacterial fitness under different environmental conditions or in different niches. Genomic islands are large chromosomal regions that have aberrant base composition compared to the whole genome, encode an integrase and insert at tRNA loci. The term ‘pathogenicity islands’ was first coined by Hacker to describe unstable regions present in pathogenic isolates of Escherichia coli that were unlike any previously described integrative element. The regions were called pathogenicity islands because they encoded several virulence factors. Subsequently, the term genomic island was introduced to describe regions that contained a diverse range of functions, such as (i) the ability to utilize novel carbon and nitrogen sources (metabolic islands); (ii) the ability to break down novel compounds (degradation islands); (iii) resistance to antibiotic and heavy metals (resistance islands); and (iv) the ability to cause disease (pathogenicity islands). Within each subset of islands, the gene content can vary considerably, even within a species.
Acquisition of genomic islands plays a central part in bacterial evolution as a mechanism of diversification and adaptation. Genomic islands are non-self-mobilizing integrative and excisive elements that encode diverse functional characteristics but all contain a recombination module comprised of an integrase, associated attachment sites and, in some cases, a recombination directionality factor. Here, we discuss how a group of related genomic islands are evolutionarily ancient elements unrelated to plasmids, phages, integrons and integrative conjugative elements. In addition, we explore the diversity of genomic islands and their insertion sites among Gram-negative bacteria and discuss why they integrate at a limited number of tRNA genes.
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The species Escherichia coli comprises non-pathogenic, commensal bacterial strains belonging to the normal gut microbiota of humans and many animals, but also pathogenic strains, which cause different types of intestinal or extraintestinal infections in man and animals. Single factors and mechanisms involved in pathogenesis of extraintestinal pathogenic E. coli (ExPEC) have been analyzed in detail for many years. Horizontal gene transfer is a key step in the evolution of bacterial pathogens. Besides phages and plasmids, pathogenicity islands (PAIs) are subjected to horizontal transfer. The transfer mechanisms of PAIs within a certain bacterial species or between different species are still not well understood.
In a new study the authors applied a phylogenetic approach using multilocus sequence typing on HPI-positive and -negative natural E. coli isolates representative of the species diversity to infer the mechanism of horizontal HPI transfer within the E. coli species. In each strain, the partial nucleotide sequences of 6 HPI–encoded genes and 6 housekeeping genes of the genomic backbone, as well as DNA fragments immediately upstream and downstream of the HPI were compared. This revealed that the HPI is not solely vertically transmitted, but that recombination of large DNA fragments beyond the HPI plays a major role in the spread of the HPI within E. coli species. In support of the results of the phylogenetic analyses, they demonstrated that HPI can be transferred between different E. coli strains by F-plasmid mediated mobilization. Sequencing of the chromosomal DNA regions immediately upstream and downstream of the HPI in the recipient strain indicated that the HPI was transferred and integrated together with HPI–flanking DNA regions of the donor strain. The results of this study demonstrate for the first time that conjugative transfer and homologous DNA recombination play a major role in horizontal transfer of a pathogenicity island within the species E. coli.
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MicroRNAs (miRNAs) are a class of small (~21–25 nucleotides) single-stranded RNAs that can inhibit the expression of specific messenger RNAs by binding to complementary target sequences within the mRNAs. Given the propensity of viruses to co-opt cellular pathways and activities for their benefit, it is perhaps not surprising that several viruses have now been shown to reshape the cellular environment by reprogramming the host’s RNA-interference machinery. In particular, microRNAs are produced by the various members of the herpesvirus family during both the latent stage of the viral life cycle and the lytic (or productive) stage. Emerging data suggest that viral microRNAs are particularly important for regulating the transition from latent to lytic replication and for attenuating antiviral immune responses.
At present, there is no evidence that any vertebrate virus encodes novel miRNA-processing factors or RISC components. So it seems that, in general, viral miRNAs are transcribed and processed in the same way as cellular miRNAs. Despite our still limited knowledge of viral miRNA functions, the large number of miRNAs that are encoded by diverse members of the herpesvirus family, and their high-level expression during latent infections, suggests that these small non-coding RNAs have a key role in regulating viral pathogenesis in vivo. In particular, it will be important to test the hypothesis that herpesvirus miRNAs that are produced during latency help to maintain the latent state, which could be examined by using viral mutants and/or antisense reagents. It certainly seems possible that antisense reagents specific for particular viral miRNAs could significantly attenuate herpesvirus-induced diseases in humans, if they could be delivered effectively to infected cells in vivo – like this!
Viral and cellular messenger RNA targets of viral microRNAs. 2009 Nature 457, 421-425
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US scientists say they have developed a cream which could for the first time prevent someone from becoming infected with genital herpes. The virus is carried by half a billion people worldwide – the disease can be controlled, but it is hard to stop it spreading to others through sex. This topical treatment, which has so far been tested only on mice, stops the virus from replicating in a new host.
Durable Protection from Herpes Simplex Virus-2 Transmission Following Intravaginal Application of siRNAs Targeting Both a Viral and Host Gene. Cell Host Microbe. 2009 Jan 22;5(1):84-94
A vaginal microbicide should prevent pathogen transmission without disrupting tissue barriers to infection. Ideally, it would not need to be applied immediately before sexual intercourse, when compliance is a problem. Intravaginal administration of small interfering RNA (siRNA) lipoplexes targeting Herpes Simplex Virus Type 2 (HSV-2) genes protects mice from HSV-2. However, protection is short-lived, and the transfection lipid on its own unacceptably enhances transmission. Here, we show that cholesterol-conjugated (chol)-siRNAs without lipid silence gene expression in the vagina without causing inflammation or inducing interferons. A viral siRNA prevents transmission within a day of challenge, whereas an siRNA targeting the HSV-2 receptor nectin-1 protects for a week, but protection is delayed for a few days until the receptor is downmodulated. Combining siRNAs targeting a viral and host gene protects mice from HSV-2 for a week, irrespective of the time of challenge. Therefore, intravaginal siRNAs could provide sustained protection against viral transmission.
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Adenoviruses are a frequent cause of acute upper respiratory tract infections, i.e. “colds”. In addition, they also cause a number of other types of infection. They were first isolated in 1953, but in 1962, some adenoviruses were shown to cause tumours in rodents – this caused a considerable panic! However adenovirus oncogenesis appears to be associated with abortive infections and has never been observed in humans. There are at least 51 human adenovirus serotypes which have been divided into subgroups A to F.
Detailed three dimensional structural models of adenovirus particles have been constructed based on a combination of cryoelectron microscopy and X-ray crystallography. There are at least 13 proteins in the adenovirus particle. All adenovirus particles are structurally similar: non-enveloped and 60-90 nm in diameter. They have icosahedral symmetry easily visible in the electron microscope by negative staining and are composed of 252 capsomers: 240 “hexons” + 12 “pentons” at vertices of icosahedron. The pentons have a toxin-like activity, purified pentons causing c.p.e. in the absence of any other virus components. A trimeric fibre protein extends from each of the 12 vertices (attached to the penton base proteins) and is responsible for recognition and binding to the cellular receptor. A globular domain at the end of the adenovirus fiber is responsible for recognition of the cellular receptor.
The adenovirus genome consists of linear, non-segmented, double-stranded DNA, 30-38 kbp long which has the capacity to encode about 40 genes. The terminal sequences of each strand are inverted repeats, hence the denatured single strands can form “panhandle” structures (100-140 bp long). There is a 55kD protein called the terminal protein (TP) covalently attached to the 5′ end of each strand.
The replication of all adenoviruses is similar and occurs in the nucleus of the host cell. Replication is divided into early and late phases, the late phase defined as beginning with the onset of DNA replication. This temporal division is characteristic of the replication of DNA viruses.
Attachment to cells is rather slow, taking several hours to reach a maximum. Uptake of the particle is a two stage process involving an initial interaction of the fibre protein with a range of cellular receptors, which include the MHC class I molecule and the coxsackievirus-adenovirus receptor. The penton base protein then binds to the integrin family of cell surface heterodimers allowing internalization via receptor-mediated endocytosis. Most cells express receptors for the adenovirus fibre coat protein, however internalisation is a more selective process. Penetration involves phagocytosis into phagocytic vacuoles, after which the toxic activity of the pentons is responsible for rupture of the phagocytic membrane and release of the particle into the cytoplasm. Uncoating follows an ordered sequence, first the pentons, releasing a spherical, partially uncoated particle into the cytoplasm. The core migrates to the nucleus where the DNA enters through nuclear pores, where it is converted into a virus DNA-cellular histone complex.
Before and independently of genome replication, immediate early and early mRNAs are transcribed from the input DNA. Transcription of the adenovirus genome is regulated by virus-encoded trans-acting regulatory factors. Products of the immediate early genes regulate expression of the early genes. Early genes are encoded at various locations on both strands of the DNA (l = “leftward strand” and r = “rightward strand”). Multiple protein products are made from each gene by alternative splicing of mRNA transcripts – splicing was first discovered in adenoviruses by Philip Sharp in 1977.
The first mRNA/protein to be made (~1h after infection) is E1A. This protein is a trans-acting transcriptional regulatory factor which is necessary for transcriptional activation of early genes. The protein is also capable of activating transcription from a variety of other virus and cellular promoters and shows no sequence-specificity, rather it causes a modification of the cellular environment. The second protein made is E1B. E1A and E1B together (and independently of other virus proteins) are capable of transforming primary cells in vitro (especially in Ad5, Ad12).
Adenovirus DNA replication has been studied extensively. At least three virus-encoded proteins are known to be involved in DNA replication:
In addition, many cellular proteins in the nucleus also participate in replication of the genome (e.g. NFI, NFII, topoisomerase I). The adenovirus genome has inverted terminal repeats (ITRs) of about 100 bp. Located within the ITRs are the cis-acting DNA sequences which define ori, the origin of DNA replication. Covalently attached to each 5′ end is a terminal protein (TP) which is an additional cis-acting component of ori.
At the onset of DNA replication, the pattern of transcription changes radically from the early to the late genes. Late phase transcription is driven primarily by the major late promoter. Although transcription from this promoter is complex involving multiple polyadenylation signals and an elaborate usage of RNA splicing, five gene clusters can be defined (L1-L5). Late phase gene expression is primarily concerned with the synthesis of virion proteins.
Particle assembly occurs in the nucleus, but begins in the cytoplasm when individual monomers form into hexon and penton capsomers. Empty, immature capsids are assembled from these protomers in the nucleus, where the core is formed from genomic DNA plus its associated core proteins.
Certain types of adenovirus are commonly associated with particular clinical syndromes. This list includes relatively common infections (at the top) and some rare infections (at the bottom). Most adenovirus infections involve either the respiratory or gastrointestinal tracts or the eye. Adenovirus infections are very common, most are asymptomatic. Most people have been infected with at least 1 type at age 15. Virus can be isolated from the majority of tonsils/adenoids surgically removed, indicating latent infections. It is not known how long the virus can persist in the body, or whether it is capable of reactivation after long periods, causing disease (it is hard to isolate this occult virus as it may be present in only a few cells). It is known that virus is reactivated during immunosuppression, e.g. in AIDS and transplant patients.
A characteristic feature of adenoviruses is their ability to subvert the host immune response by using the early E3 cassette of genes. The E3 membrane proteins are able to downregulate critical recognition structures for the host immune system from the cell surface.
There is no treatment available for adenovirus infections. Inactivated vaccines have been developed and are routinely used for military recruits in some countries (notably the USA). This is because adolescents and others in close daily contact are at risk for epidemic spread of respiratory infections, but the risk to general population is so low that vaccination is not a viable proposition.
In recent years, there has been considerable interest in developing adenoviruses as defective vectors to carry and express foreign genes for therapeutic purposes. One reason for this is that the adenovirus genome is relatively easily manipulated in vitro (c.f. retroviruses) and the genes coupled to the late promoter are efficiently expressed in large amounts. Adenoviruses have been studied intensively for over 50 years as models of virus-cell interactions and more recently as gene vectors.
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What is genomics? How will it affect our lives? In this primer on the genomics revolution, entrepreneur Barry Schuler says we can at least expect healthier, tastier food. He suggests we start with the pinot noir grape, to build better wines.
A patient is being treated for Lassa fever at the high security infectious diseases unit at the Royal Free Hospital in London. The Health Protection Agency say this is an isolated case in a traveller who returned to the UK from Nigeria. They are trying to identify nurses and doctors at two other hospitals who cared for the man before the disease was identified. Lassa fever is spread through direct contact with body fluids.
Nearly 35 million people across the globe are infected with the human immunodeficiency virus type 1 (HIV-1) and an additional 2.5 million new infections occur annually. The current pandemic is the result of viruses that are genetically diverse and have been divided into 9 different subtypes and at least 28 circulating recombinant forms. The mechanisms by which HIV-1 is transmitted sexually across a mucosal barrier remain poorly understood.
Previous studies of HIV transmission have yielded conflicting results regarding the genetic heterogeneity of the virus establishing infection in the newly infected individual. The new results explain why prior infection by other sexually-transmitted diseases (STDs) makes individuals more susceptible to HIV infection. The team of researchers identified 20 heterosexual couples soon after infection occurred and obtained virus genetic sequences from both partners. They examined the most variable region of the virus’ env gene, which encodes a protein on the outer coat of the virus. Approximately 90% of the couples were found to be infected by a single virus variant of HIV-1. However, that variant was not the same in each case. For comparison, the researchers also analyzed a group of newly infected individuals who were infected by someone other than their spouse. This group showed more variety in virus sequences, with 3 out of 7 individuals infected by multiple variants. The homogeneity of the virus population in the newly infected recipient, as well as the presence, in some cases, of identical virus variants in the donor, allowed them to precisely identify the transmitted variant.
Overall, out of 42 newly infected people studied to date, all five infected by multiple virus variants had evidence of genital inflammation or ulceration. In these cases, it appears that the bottleneck was enlarged due to the disruption of normally protective mucosal barriers by STDs. They were able to examine the clinical history of each newly infected individual and observed that all individuals infected by multiple variants also showed evidence of inflammatory genital infections. These findings suggest that the genital mucosa provides a natural barrier to infection by multiple genetic variants of HIV-1 that can be lowered by inflammatory genital infections.
Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1. PLoS Pathog 5(1): e1000274
The HIV-1 epidemic in sub-Saharan Africa is driven largely by heterosexual transmission of non-subtype B viruses, of which subtypes C and A are predominant. Previous studies of subtype B and subtype C transmission pairs have suggested that a single variant from the chronically infected partner can establish infection in their newly infected partner. However, in subtype A infected individuals from a sex worker cohort and subtype B individuals from STD clinics, infection was frequently established by multiple variants. This study examined over 1750 single-genome amplified viral sequences derived from epidemiologically linked subtype C and subtype A transmission pairs very early after infection. In 90% (18/20) of the pairs, HIV-1 infection is initiated by a single viral variant that is derived from the quasispecies of the transmitting partner. In addition, the virus initiating infection in individuals who were infected by someone other than their spouse was characterized to determine if genital infections mitigated the severe genetic bottleneck observed in a majority of epidemiologically linked heterosexual HIV-1 transmission events. In nearly 50% (3/7) of individuals infected by someone other than their spouse, multiple genetic variants from a single individual established infection. A statistically significant association was observed between infection by multiple genetic variants and an inflammatory genital infection in the newly infected individual. Thus, in the vast majority of HIV-1 transmission events in cohabiting heterosexual couples, a single genetic variant establishes infection. Nevertheless, this severe genetic bottleneck can be mitigated by the presence of inflammatory genital infections in the at risk partner, suggesting that this restriction on genetic diversity is imposed in large part by the mucosal barrier.
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