Evolution. Little else but parasites.
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Alleles↗
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Microbiology. Unlocking the secrets of the grim reaper.
On page 1594, researchers unveil the workings of YopJ, one of a group of nefarious proteins that Yersinia bacteria--including Y. pestis, the bacterium that is infamous for causing the bubonic plague--deploy. Early in the disease, Yersinia bacteria inject YopJ into macrophage cells of the immune system, where, the researchers have now found, YopJ acts like scissors, cleaving the macrophage proteins that would normally send an SOS to other immune cells for help. Leaving the macrophage stranded clears the way for other Yersinia proteins to destroy the cell.
Animals↗
Infectious diseases. Darwinian vaccines.
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Biological Evolution↗
Cryptococcus neoformans capsule structure evolution in vitro and during murine infection.
Cryptococcus neoformans capsule structure modifications after prolonged in vitro growth or in vivo passaging have been reported previously. However, nothing is known about the dynamics of these modifications or about their environmental specificities. In this study, capsule structure modifications after mouse passaging and prolonged in vitro culturing were analyzed by flow cytometry using the glucuronoxylomannan-specific monoclonal antibody E1. The capsule structures of strains recovered after 0, 1, 8, and 35 days were compared by using the level of E1-specific epitope expression and its cell-to-cell heterogeneity within a given cell population. In vitro, according to these parameters, the diversity of the strains was higher on day 35 than it was initially, suggesting the absence of selection during in vitro culturing. In contrast, the diversity of the strains recovered from the brain tended to decrease over time, suggesting that selection of more adapted strains had occurred. The strains recovered on day 35 from the spleen and the lungs had different phenotypes than the strains isolated from the brain of the same mouse on the same day, thus strongly suggesting that there is organ specificity for C. neoformans strain selection. Fingerprinting of the strains recovered in vitro and in vivo over time confirmed that genotypes evolved very differently in vitro and in vivo, depending on the environment. Overall, our results suggest that organ-specific selection can occur during cryptococcosis.
Animals↗
Structural and genetic diversity of group B streptococcus capsular polysaccharides.
Group B Streptococcus (GBS) is an important pathogen of neonates, pregnant women, and immunocompromised individuals. GBS isolates associated with human infection produce one of nine antigenically distinct capsular polysaccharides which are thought to play a key role in virulence. A comparison of GBS polysaccharide structures of all nine known GBS serotypes together with the predicted amino acid sequences of the proteins that direct their synthesis suggests that the evolution of serotype-specific capsular polysaccharides has proceeded through en bloc replacement of individual glycosyltransferase genes with DNA sequences that encode enzymes with new linkage specificities. We found striking heterogeneity in amino acid sequences of synthetic enzymes with very similar functions, an observation that supports horizontal gene transfer rather than stepwise mutagenesis as a mechanism for capsule variation. Eight of the nine serotypes appear to be closely related both structurally and genetically, whereas serotype VIII is more distantly related. This similarity in polysaccharide structure strongly suggests that the evolutionary pressure toward antigenic variation exerted by acquired immunity is counterbalanced by a survival advantage conferred by conserved structural motifs of the GBS polysaccharides.
Bacterial Capsules↗
Evolutionary origin of pathogenic determinants in enterotoxigenic Escherichia coli and Vibrio cholerae O1.
Three families of the evolutionarily related pathogenic determinants in enterotoxigenic Escherichia coli and Vibrio cholerae O1, a family of cholera enterotoxin (CT) and heat-labile enterotoxin (LT) including CT, LTh, and LTp, a family of heat-stable enterotoxin I (STI) including STIa and STIb, and a family of K88 enteroadhesion fimbriae including K88ab, K88ac, and K88ad were analyzed for synonymous (silent) nucleotide substitutions by using the gene nucleotide sequences of earlier reports and the LTp gene nucleotide sequence presented in this paper. The data suggested that the divergences between LT and CT and between STIa and STIb occurred in the remote past, whereas those between LTh and LTp and between members of the K88 family occurred very recently. We concluded that the LT gene is a foreign gene that has been acquired by E. coli to form an enteropathogen. This provides evolutionary evidence of species-to-species transfer of pathogenic determinants in procaryotes.
Base Sequence↗
MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism.
Since the discovery of microRNA (miRNA)-guided processing, a new type of RNA silencing, the possibility that such a mechanism could play a role in virus defense has been proposed. In this work, we have analyzed whether Plum pox virus (PPV) chimeras bearing miRNA target sequences (miR171, miR167, and miR159), which have been reported to be functional in Arabidopsis, were affected by miRNA function in three different host plants. Some of these PPV chimeras had clearly impaired infectivity compared with those carrying nonfunctional miRNA target sequences. The behaviors of PPV chimeras were similar but not identical in all the plants tested, and the deleterious effect on virus infectivity depended on the miRNA sequence cloned and on the site of insertion in the viral genome. The effect of the miRNA target sequence was drastically alleviated in transgenic plants expressing the silencing suppressor P1/HCPro. Furthermore, we show that virus chimeras readily escape RNA silencing interference through mutations within the miRNA target sequence, which mainly affected nucleotides matching the 5'-terminal region of the miRNA.
Arabidopsis↗
Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid).
BACKGROUND: Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc. RESULTS: Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species. CONCLUSIONS: The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.
Amino Acid Sequence↗
Probing orthobunyavirus reassortment using Bunyamwera and Batai viruses as models.
Reassortment is a critical evolutionary mechanism for segmented viruses, enabling the exchange of intact genome segments during co-infection and driving orthobunyavirus evolution; however, the molecular mechanisms underpinning this process remain unclear. With over 100 orthobunyavirus species, many of which are significant human and veterinary pathogens, understanding how reassortment influences transmissibility and virulence is essential for preempting the emergence of novel pathogens. Here, we use Bunyamwera virus (BUNV) and Batai virus (BATV) as models to explore orthobunyavirus reassortment through reverse genetics. We established the first reverse genetics system for BATV, generated reassortants, and employed minigenome assays to assess replication machinery compatibility. Additionally, we developed a novel hybridization chain reaction assay for high-resolution visualization of viral RNA segments. Our findings revealed that all six reassortants between BUNV and BATV are viable, exhibiting notable phenotypic differences in interferon-deficient (IFNAR-/-) mice. This work introduces essential tools and new insights into orthobunyavirus reassortment and pathogenesis, laying the groundwork for understanding this critical evolutionary process.
Animals↗
Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana.
Species-level genetic diversity and recombination in bacterial pathogens of wild plant populations have been nearly unexplored. Pseudomonas viridiflava is a common natural bacterial pathogen of Arabidopsis thaliana, for which pathogen defense genes and mechanisms are becoming increasing well known. The genetic variation contained within a worldwide sample of P. viridiflava collected from wild populations of A. thaliana was investigated using five genomic sequence fragments totaling 2.3 kb. Two distinct and deeply diverged clades were found within the P. viridiflava sample and in close proximity in multiple populations, each genetically diverse with synonymous variation as high as 9.3% in one of these clades. Within clades, there is evidence of frequent recombination within and between each sequenced locus and little geographic differentiation. Isolates from both clades were also found in a small sample of other herbaceous species in Midwest populations, indicating a possibly broad host range for P. viridiflava. The high levels of genetic variation and recombination together with a lack of geographic differentiation in this pathogen distinguish it from other bacterial plant pathogens for which intraspecific variation has been examined.
Arabidopsis↗
Viroids: unusual small pathogenic RNAs.
Viroids are small (about 300 nucleotides), single-stranded, circular, non-encapsidated pathogenic RNA molecules. They do not code for proteins and thus depend on plant host enzymes for their replication and other functions. They induce plant diseases by direct interaction with host factors but the mechanism of pathogenicity is still unknown. They can alter the expression of selected plant genes important for growth and development. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Viroids of the Avsunviroidae family adopt a branched or quasi rod-like secondary structure in their native state. Members of the Pospiviroidae family adopt a rod-like secondary structure. In such native structures five structural/functional domains have been identified: central (C), pathogenicity, variable and two terminal domains. The central conserved region (CCR) within the C domain characterizes viroids of the Pospiviroidae. Specific secondary structures of this region play an important role in viroid replication and processing. Viroids of the Avsunviroidae family lack a CCR but possess self-cleaving properties by forming hammerhead ribozyme structures; they accumulate and replicate in chloroplasts, whereas members of the Pospiviroidae family have a nuclear localization. Viroid replication occurs via a rolling circle mechanism using either a symmetric or asymmetric pathway in three steps, RNA transcription, processing and ligation.
Base Sequence↗
[Epidemiologic aspects of the anthroponotic concept of the origin of pandemic and epidemic strains of influenza A virus].
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Antigens, Heterophile↗
Molecular biology of Entamoeba histolytica: a review.
Amebiasis is one of the main causes worldwide of morbidity and mortality by parasites. Application of recombinant DNA technology to the study of Entamoeba histolytica is bringing new light into our understanding of this remarkable protozoan parasite and of the disease it causes. New achievements affect the way we approach many essential questions about E. histolytica, from the mechanism of its pathogenicity to the definition of E. histolytica as a separate species from the nonpathogenic E. dispar. To give a single example, transfection of trophozoites is now possible and a new generation of studies taking advantage of this capability of manipulation is expected in the short term. Our goal with this review is to provide an updated and simple guide to the growing information on the molecular biology of E. histolytica.
Anaerobiosis↗
Host hybridization enabled the emergence of a reassorted hantavirus lineage.
The exchange of genetic material between individuals is a key driver of evolution and diversification across most branches of life. Segmented viruses can exchange genetic material through reassortment of genomic segments. New viral strains that emerge from reassortments can have greater infection ranges and higher virulence, although concrete examples of the adaptive advantages of reassortants in nature apart from influenza remain rare. We studied here the evolutionary history and consequences of reassortment in Tula orthohantavirus (TULV) in a hybrid zone between evolutionary lineages of its reservoir host, the common vole (Microtus arvalis). Across 58 trapping sites and 127 infected voles, we detected 27 TULV reassortants in a 12.5 km broad zone at the contact of the parental TULV clades, resembling a viral hybrid zone concordant with the hosts'. Phylogenomic analyses revealed three independent reassortment events, but most of the host hybrid zone was dominated by a single strain with a reassorted M-Segment, which encodes the surface glycoprotein. We detected clade-specific variation in the glycoprotein's N-terminal region consisting of five residues, two of which showed evidence of positive selection. In silico 3D modeling of seven glycoproteins confirmed that this N-terminal region has a unique and specific structure for each TULV clade and the dominant reassortants and is the only structurally variable region of the TULV glycoprotein. Our findings suggest that reassortment between the parental TULV clades in the contact region has resulted in a transgressive virus phenotype potentially adapted to hybrid hosts. This demonstrates the potential of zones of hybridization for the emergence of new virus strains with novel evolutionary trajectories.
Animals↗
Genome sequence of Yersinia pestis, the causative agent of plague.
The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.
Animals↗
Molecular characteristics and epidemiological significance of Shiga toxin-producing Escherichia coli O26 strains.
Fifty-five Shiga toxin (Stx)-producing Escherichia coli (STEC) O26:H11 and O26:H(-) strains isolated from humans between 1965 and 1999 in Germany and the Czech Republic were investigated for their chromosomal and plasmid characteristics. All motile (n = 23) and nonmotile (n = 32) STEC O26 strains were shown to possess the identical flagellin subunit-encoding gene (fliC). We observed a striking recent shift of the stx genotype from stx(1) to stx(2) among the STEC O26 isolates. While stx(1) was the exclusive genotype identified in our collection until 1994, 94% of the isolates obtained after 1997 possessed stx(2) either alone (71%) or together with stx(1) (23%). Plasmid profiling demonstrated a remarkable heterogeneity with respect to plasmid sizes and combinations. Southern blot analysis of plasmid DNA with probes specific to potential accessory virulence genes revealed considerable additional variability in gene composition and arrangement. Pulsed-field gel electrophoresis (PFGE) differentiated 16 subgroups among the 55 STEC O26 strains. Using these techniques we demonstrate the emergence of a new clonal subgroup characterized by PFGE pattern A and a unique combination of virulence markers including stx(2) and a single, approximately 90-kb plasmid harboring the enterhemorrhagic E. coli hlyA and etp genes. The proportion of PFGE subgroup A strains among STEC O26 isolates rose from 30% in 1996 to more than 50% in 1999. Four clusters of infections with the clonal subgroup A were identified. We conclude that the STEC serogroup O26 is diverse and that pathogenic clonal subgroups can rapidly emerge during short intervals. The extensive genetic diversity of STEC O26 provides a basis for molecular subtyping of this important non-O157 STEC serogroup.
Bacterial Toxins↗
Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains.
Clostridium difficile is the most frequent cause of nosocomial diarrhea worldwide, and recent reports suggested the emergence of a hypervirulent strain in North America and Europe. In this study, we applied comparative phylogenomics (whole-genome comparisons using DNA microarrays combined with Bayesian phylogenies) to model the phylogeny of C. difficile, including 75 diverse isolates comprising hypervirulent, toxin-variable, and animal strains. The analysis identified four distinct statistically supported clusters comprising a hypervirulent clade, a toxin A(-) B(+) clade, and two clades with human and animal isolates. Genetic differences among clades revealed several genetic islands relating to virulence and niche adaptation, including antibiotic resistance, motility, adhesion, and enteric metabolism. Only 19.7% of genes were shared by all strains, confirming that this enteric species readily undergoes genetic exchange. This study has provided insight into the possible origins of C. difficile and its evolution that may have implications in disease control strategies.
Animals↗
Staphylococcus aureus outbreaks among newborns: new frontiers in an old dilemma.
The acquisition of Staphylococcus aureus by the newborn in the early neonatal period is common. Most such acquisitions are not followed by infection, although the potential for serious infection increases in the intensive care unit setting. Attack rates for infection are quite variable, but outbreaks have occurred on many occasions. Although some bacterial virulence factors, such as exfoliative toxins, are associated with outbreaks, most epidemic strains do not have well-defined virulence factors that can be incriminated. There are many possible control measures, but the implementation of these are balanced by the existing circumstances and perceived cost. As methicillin-resistant S. aureus (MRSA) becomes endemic in hospital settings, these bacteria are becoming much more common in nursery outbreaks. Over time, antibiotic selection and enhanced disease causation will lead to the evolution of hypervirulent MRSA clones. The latter will become an increasing problem unless effectively controlled.
Disease Outbreaks↗