The Landscape of Realized Homologous Recombination in Pathogenic Bacteria

Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have “hot” regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several eukaryotes. Genes with function related to the cell surface/membrane are often found in recombination hot regions but E. coli is the only species where genes annotated as “virulence associated” are consistently hotter. There is also evidence that some genes with “housekeeping” functions tend to be overrepresented in cold regions. For example, ribosomal proteins showed low recombination in all of the species. Among specific genes, transferrin-binding proteins are recombination hot in all three of the species in which they were found, and are subject to interspecies recombination

Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and Restriction-Modification System

The necessity to repair genome damage has been considered to be an immediate factor responsible for the origin of sex. Indeed, attack by a cellular restriction enzyme of invading DNA from several bacteriophages initiates recombinational repair by gene conversion if there is homologous DNA. In the present work, we modeled the interaction between a bacteriophage and a bacterium carrying a restriction enzyme as antagonistic coevolution. We assume a locus on the bacteriophage genome has either a restriction-sensitive or a -resistant allele, and another locus determines whether it is recombination/repair-proficient or -defective. A restriction break can be repaired by a co-infecting phage genome if one of them is recombination/repair-proficient. We define the fitness of phage (resistant/sensitive and repair-positive/-negative) genotypes and bacterial (restriction-positive/-negative) genotypes by assuming random encounter of the genotypes, with a given probabilities of single and double infections, and the costs of resistance, repair and restriction. Our results show the evolution of the repair allele depends on b1 / b0 , the ratio of the burst size b1 under damage to host cell physiology induced by an unrepaired double-strand break to the default burst size b0 . It was not until this effect was taken into account that the evolutionary advantage of DNA repair became apparent

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS > 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication, recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures. Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination. We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes

Status, trends and future dynamics of biodiversity and ecosystems underpinning nature's contributions to people

Biodiversity at the species and ecosystem levels is currently under multiple threats almost everywhere in the Asia-Pacific region, and in many areas the situation is now critical (well established). Of the various ecosystems, lowland evergreen forests, alpine ecosystems, limestone karsts, inland wetlands, and estuarine and coastal habitats are most threatened (well established). Genetic diversity within species, both wild and domestic, is also decreasing in many cases as a result of decreasing ranges (established but incomplete). In several countries there has been a small increase in the forest cover which is mostly attributed to monoculture forestry plantations and enabling policies of the governments. Forest fires associated with rapid loss of forest cover is leading to enormous environmental and socio-economic loss (well established) {3.2.1; 3.2.2; 3.2.3; 3.2.4; 3.2.5; 3.3.1}. There has been a steady decline in the populations of large vertebrates due to poaching and illegal trade in wildlife parts and products in the Asia-Pacific region (well established). As a result, most of these species now survive only in the best-managed protected areas (well established). Widespread loss of large vertebrates has had a measureable impact on several forest functions and services, including seed dispersal (established but incomplete). Australia has the highest rate of mammal extinction (>10 per cent) of any continent globally. Bird extinctions on individual Pacific islands range from 15.4 per cent to 87.5 per cent for those with good fossil records, and these extinctions have resulted in the loss of many ecological functions previously performed by birds (well established). Besides wildlife, there is a massive regional trade in timber, traditional medicines and other products (well established). Without adequate protection, remediation and proper policies, the current decline in biodiversity and nature's contributions to people on land, in freshwaters, and in the sea will threaten the quality of life of future generations in the Asia-Pacific region {3.2.1.1; 3.2.1.2; 3.2.1.4; 3.2.1.7; 3.2.2.1; 3.3.1} With the current rate of human population growth, expansion of urban industrial environments, transformation of agriculture in favour of high yielding varieties, transforming forests to uniform plantations of oil palm, rubber or timber trees, the biodiversity and nature's contributions to people in the Asia-Pacific region are likely to be adversely affected in the coming decades (well established). It is predicted that most of the biodiversity in the next few decades may be confined to protected areas or in places where the local communities have taken the lead in local level conservation in lieu of economic incentives and equitable compensation by the stake-holders. Unprecedented increase in human population of the Asia-Pacific region has stressed the fragile ecosystems to their limits; while arable cropping has been extended to sites which were not entirely suitable for it, resulting in soil degradation and erosion (well established) {3.2.1.1; 3.2.1.2; 3.2.1.5; 3.2.2.2; 3.2.2.4; 3.3; 3.3.1; 3.3.6; 3.4}. Freshwater ecosystems in the Asia-Pacific region support more than 28 per cent of aquatic and semi-aquatic species but nearly 37 per cent of these species are threatened due to anthropogenic and climatic drivers (well established). Cumulative impacts of global warming and damming of rivers in some of the river basins will have significant negative impacts on fish production and environmental flows (well established). Likewise, degradation of wetlands has had severe negative impacts on migratory waterfowl, fish production and local livelihoods (well established). However, there are scientific data gaps on the current status of biodiversity and nature's contributions to people in most of the river basins, inland wetlands and peatlands of the region {3.2.2.1; 3.2.2.2; 3.2.2.3; 3.2.2.4}. Coastal and marine habitats are likewise threatened due to commercial aquaculture, overfishing, and pollution affecting biodiversity and nature's contributions to people (well established). Detailed analyses of fisheries production in the region have shown severe decline in recent decades. It is projected that if unsustainable fishing practices continue, there could be no exploitable stocks of fish by as early as 2048. This could lead to trophic cascades and collapse of marine ecosystems (established but incomplete). Loss of seagrass beds which forms main diet of several threatened species such as dugong is a major concern (well established). There is a need to conduct systematic and region-wide assessment of fisheries stocks and coastal habitat in the region to aid conservation, management and restoration. {3.1.3.1; 3.2.3.3; 3.2.3.6; 3.2.4.6; 3.4}. Mangrove ecosystems in the Asia-Pacific region are most diverse in the world. They support a rich biodiversity and provide a range of provisioning, regulating and supporting services, which are crucial for the livelihood of local communities (well established). Both mangrove and intertidal habitats form a buffer from siltation for offshore coral reefs protection hence affecting productivity of reefs including seagrass. However, up to 75 per cent of the mangroves have been degraded or converted in recent decades (well established). The conversion of mangroves to aquaculture, rice, oil palm, and other land-use changes is leading to the loss of the buffer between sea and land which can reduce the impact of natural disasters such as cyclones and tsunamis. It is projected that rise in sea level due to global warming would pose the biggest threat to mangroves, thereby affecting nature's contributions to people especially in Bangladesh, Philippines, New Zealand, Viet Nam and China (well established) {3.2.3.1; 3.2.3.2; 3.3.4}. There has been a steady increase in the number, abundance and impacts of invasive alien species in the Asia-Pacific region, negatively affecting native biodiversity, ecosystem functioning and socio-cultural environments (well established). The total annual loss caused by invasive alien species has been estimated at US$35.5 billion in SE Asia and US$9B in Australia. Costs to agriculture due to invasive alien species are likewise immense in the region {3.2.1.1; 3.2.1.2; 3.2.1.4; 3.2.1.5; 3.2.1.6; 3.2.1.7; 3.2.2.1; 3.2.2.2; 3.2.2.3; 3.2.3.6; 3.3.5}. There has been a nearly 30 per cent decline in biocultural diversity in the Asia-Pacific region since the 1970s (well established). Decline of linguistic diversity has been catastrophic in the indigenous Australian and Trans-New Guinean families, as a result of a shifting away from small indigenous languages towards larger, national or regional languages (well established). Linguistic and biological diversity often coincide in the Asia-Pacific region and parallel strategies need to be developed for their conservation. National conservation priorities should take into consideration the bioculturally rich areas that are facing great threats {3.2.5; 3.2.5.2; 3.2.5.4; 3.4}. Protected Area coverage in the Asia-Pacific region has increased substantially since last three decades. Despite this progress, however, at least 75 per cent of Key Biodiversity Areas remain unprotected, suggesting that the region is not on track to conserve areas of particular importance for biodiversity, as called for under Aichi Target 11 (well established). Oceania has the highest overall Protected Area coverage in the region. North-East Asia has the highest proportion of Key Biodiversity Areas covered by Protected Areas, but only 1 per cent of its marine area is protected (well established) {3.2.5.6; 3.2.6; 3.2.6.1}. The Asia-Pacific region has high levels of endemism, and some 25 per cent of the region’s endemic species are facing high extinction risks as per the IUCN Red List. Endemic species in some subregions face an extinction risk as high as 46 per cent of endemic species threatened in South Asia (well established). South-East Asia has the greatest number of threatened species and the fastest increases in extinction risk (Red List Index) in the Asia-Pacific region. North Asian endemic species extinction risk is also higher than the regional average; the high percentage of Data Deficient species (36 per cent) indicates that more research and conservation action are needed for endemic species in this subregion (well established) {3.2.1; 3.2.2; 3.2.6.2; 3.3.4}. Some aspects of biodiversity have recently started to recover in several countries in the Asia-Pacific region (established but incomplete). This recovery has resulted from various changes, including population concentration in cities, increased agricultural production per unit area, increasing conservation awareness among citizens, and the enabling policies of the governments. Future trends of biodiversity in the Asia-Pacific region will largely depend on whether other countries will follow this recovering trajectory by stabilizing land/sea use change, manage their natural resources sustainably, and cooperating with each other in meeting the Aichi Targets and the Sustainable Development Goals {3.2.1.5; 3.2.3.5; 3.3.1; 3.3.3; 3.3.6}. Given that the scientific information on the status and trends of biodiversity and nature's contributions to people is not available uniformly across all ecosystems and habitats in the region, the national governments are encouraged to initiate systematic documentation and monitoring of health of ecosystems and ecosystem flows (established but incomplete). Saving terrestrial fauna especially big mammals and other fauna that require large roaming areas such as Orangutans, proboscis monkey, hornbills, tigers, Sumatran rhinoceros, gaurs and Asian elephants can be done by connecting large tracts of forests with wildlife corridors or through rehabilitation projects; the same goes for coastal and marine, freshwater and other ecosystems in the region {3.2.1.1; 3.2.2.4; 3.3.4; 3.4}

Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins

We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The gentic diversity of H pylori is known to be influenced by these genomic elements including prophages who’s geneomes range from 22.6 to 33.0 Kbp. There was a high conservation of integration site shared in over 50% of cases with greater than 40% or prophage genomes harbouring insertion sequences (IS). Furthermore prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. There was evidence of recombination within the genome of some prophages, which resulted in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes

Identification of biomolecule mass transport and binding rate parameters in living cells by inverse modeling

BACKGROUND: Quantification of in-vivo biomolecule mass transport and reaction rate parameters from experimental data obtained by Fluorescence Recovery after Photobleaching (FRAP) is becoming more important. METHODS AND RESULTS: The Osborne-Moré extended version of the Levenberg-Marquardt optimization algorithm was coupled with the experimental data obtained by the Fluorescence Recovery after Photobleaching (FRAP) protocol, and the numerical solution of a set of two partial differential equations governing macromolecule mass transport and reaction in living cells, to inversely estimate optimized values of the molecular diffusion coefficient and binding rate parameters of GFP-tagged glucocorticoid receptor. The results indicate that the FRAP protocol provides enough information to estimate one parameter uniquely using a nonlinear optimization technique. Coupling FRAP experimental data with the inverse modeling strategy, one can also uniquely estimate the individual values of the binding rate coefficients if the molecular diffusion coefficient is known. One can also simultaneously estimate the dissociation rate parameter and molecular diffusion coefficient given the pseudo-association rate parameter is known. However, the protocol provides insufficient information for unique simultaneous estimation of three parameters (diffusion coefficient and binding rate parameters) owing to the high intercorrelation between the molecular diffusion coefficient and pseudo-association rate parameter. Attempts to estimate macromolecule mass transport and binding rate parameters simultaneously from FRAP data result in misleading conclusions regarding concentrations of free macromolecule and bound complex inside the cell, average binding time per vacant site, average time for diffusion of macromolecules from one site to the next, and slow or rapid mobility of biomolecules in cells. CONCLUSION: To obtain unique values for molecular diffusion coefficient and binding rate parameters from FRAP data, we propose conducting two FRAP experiments on the same class of macromolecule and cell. One experiment should be used to measure the molecular diffusion coefficient independently of binding in an effective diffusion regime and the other should be conducted in a reaction dominant or reaction-diffusion regime to quantify binding rate parameters. The method described in this paper is likely to be widely used to estimate in-vivo biomolecule mass transport and binding rate parameters