MicrobiologyBytes

In Sneeze, you are a virus in a human and have the opportunity the spread yourself in various environments by having your human sneeze just once on each level…

Studies using model organisms have pointed to the existence of evolutionarily conserved genes and signaling pathways that regulate life span. Changes in the activity of these genes/pathways have also been implicated in mediating the beneficial effect of calorie restriction, a well recognized intervention that extends the life span from yeast to mammals. Researchers investigated the global gene expression changes and identified genes involved in the metabolism of various kinds of carbon sources that are associated with longevity in the single cell organism, the baker’s yeast Saccharomyces cerevisiae. Although glucose and ethanol are common carbon sources for growth, they also have detrimental pro-aging effects in yeast. Long-lived yeast mutants actively utilize available glucose and ethanol and produce glycerol, which does not adversely affect the yeast life span extension. New findings suggest that this “carbon source substitution” observed in long-lived yeast creates an environment mimicking calorie restriction, which together with the direct regulation of stress resistance systems optimizes life span extension.

Yeast maintained on a glycerol diet live twice as long as normal – as long as yeast cells on a severe caloric-restriction diet. They are also more resistant to cell damage. Many studies have shown that caloric restriction can extend the life span of a variety of laboratory animals. Caloric restriction is also known to cause major improvements in a number of markers for cardiovascular diseases in humans. This study is the first to propose that “dietary substitution” can replace “dietary restriction” in a living species. If you add glycerol, or restrict caloric intake, you obtain the same effect. This is as effective as calorie restriction, yet cells can take it up and utilize it to generate energy or for the synthesis of cellular components.

The researchers investigated the effect of a glycerol diet after discovering that genetically engineered long-lived yeast cells that survive up to 5-fold longer than normal have increased levels of the genes that produce glycerol. In fact, they convert virtually all the glucose and ethanol into glycerol. Notably, these cells have a reduced activity in the TOR1/SCH9 pathway, which is also believed to extend life span in organisms ranging from worms to mice. When the researchers blocked the genes that produce glycerol, the cells lost most of their life span advantage. However, the “glucose to glycerol” switch is believed to represent only one component of the protective systems required for extended survival. This study indicates that glycerol biosynthesis is an important process in the metabolic switch that allows this simple organism to activate its protective systems and live longer. This is a fundamental observation in a very simple system, that at least introduces the possibility that you don’t have to be calorie-restricted to achieve some of the remarkable protective effects of the hypocaloric diet observed in many organisms, including humans. It may be sufficient to substitute the carbon source and possibly other macronutrients with nutrients that do not promote the “pro-aging” changes induced by sugars. Findings using these simple genetic models should help to discover fundamental longevity regulatory mechanisms and identify similar pathways in mammals. Darn useful things, yeasts :-)

Tor1/Sch9-Regulated Carbon Source Substitution Is as Effective as Calorie Restriction in Life Span Extension. PLoS Genet 5(5): e1000467
The effect of calorie restriction (CR) on life span extension, demonstrated in organisms ranging from yeast to mice, may involve the down-regulation of pathways, including Tor, Akt, and Ras. Here, we present data suggesting that yeast Tor1 and Sch9 (a homolog of the mammalian kinases Akt and S6K) is a central component of a network that controls a common set of genes implicated in a metabolic switch from the TCA cycle and respiration to glycolysis and glycerol biosynthesis. During chronological survival, mutants lacking SCH9 depleted extracellular ethanol and reduced stored lipids, but synthesized and released glycerol. Deletion of the glycerol biosynthesis genes GPD1, GPD2, or RHR2, among the most up-regulated in longlived sch9D, tor1D, and ras2D mutants, was sufficient to reverse chronological life span extension in sch9D mutants, suggesting that glycerol production, in addition to the regulation of stress resistance systems, optimizes life span extension. Glycerol, unlike glucose or ethanol, did not adversely affect the life span extension induced by calorie restriction or starvation, suggesting that carbon source substitution may represent an alternative to calorie restriction as a strategy to delay aging.

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Transcription, the process of converting DNA into RNA (which in turn is translated into proteins by ribosomes) is carried out by the multisubunit RNA polymerase (RNAP) enzyme. Transcription is fundamental to all organisms across the three kingdoms of life – Eukarya, Bacteria, and Archaea – and can be divided into three major steps: initiation, transcription/elongation, and termination. Eukaryotes have three different nuclear RNAPs, whereas Archaea and Bacteria have one. Archaeal transcription is similar to that of eukaryotes, but initiation requires only two accessory proteins bound to DNA: transcription factor B (TFB) and TATA-box binding protein (TBP). It is believed that studies of the archaeal enzyme may shed light on the more complex eukaryotic RNAP. New research has shown that organisms which live in boiling acid read their DNA using enzymes surprisingly similar to our own, providing insight into the way in which the information stored in DNA is unlocked. This new work has shown that the enzyme that converts DNA into RNA is conserved between simple single-celled microorganism Sulfolobus and more complicated “higher” organisms, including human beings, despite a staggering 2 billion year evolutionary gulf. A new paper explores how evolution has shaped our own RNAP enzyme to accomplish more complex functions.

Many Archaea are extremophiles; living in high salt, acid or temperature environments. Transcription, the process of reading DNA to make RNA (which is in turn translated into proteins by ribosomes) is a fundamental process common to all organisms, and is carried out by the enzyme multisubunit RNA polymerase (RNAP). Eukaryotes have three different RNAPs, whereas Archaea and Bacteria have one. Archaea can serve as a wonderful model system because their simpler RNA polymerase machinery is related to the more complex eukaryotic RNAP. To start transcription, the archaeal enzyme requires two accessory proteins whilst the eukaryotic counterpart needs at least two more. This increased complexity prompts two important questions: how did our polymerase evolve from the ancestral enzyme; and how does Archaea bypass the requirement of further co-factor proteins?

New work investigates the polymerase from the Archaeon Sulfolobus shibatae using X-ray crystallography. This reveals the enzyme’s architecture which confirms its close evolutionary relationship with the eukaryotic RNAP. The research also identified a subunit novel to Sulfolobus which has no equivalent in the eukaryotic enzyme. The striking structural similarities suggest that the ancestral eukaryote used the same enzyme as the Archaeon, and that modern eukaryotic RNAP evolved by the addition of bolt-on proteins that regulate eukaryotic-specific processes. From the location and topology of the newly identified, Archaeon-only subunit, the scientists have suggested a mechanism by which Archaea do without the additional cofactors required by eukaryotes for initiating transcription. The scientists also noted that the complete structure of the archaeal polymerase illustrates how the ancestral core enzyme was modulated by addition of novel subunits, an evolutionary process that has facilitated the complexity that we see today in Eukarya.

Evolution of complex RNA polymerases: The complete archaeal RNA polymerase structure. 2009 PLoS Biol 7(5): e1000102
The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 A° resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA9/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.

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Aedes (Stegomyia) aegypti (Linneaus) is an important vector of dengue and other arboviruses. Despite its limited flight dispersal capability, its close association with humans and its desiccation-resistant eggs have facilitated many long distance dispersal events within and between continents, allowing it to expand its range globally from its origin in Africa. Its global emergence and resurgence can be attributed to factors including urbanisation, transportation, changes in human movement, and behaviour, resulting in dengue running second to malaria in terms of human morbidity and mortality. Global historical collections and laboratory experiments on this well studied vector have suggested its distribution is limited by the 10°C winter isotherm, while a more recent and complex stochastic population dynamics model analysis suggests the temperature’s limiting value to be more towards the 15°C yearly isotherm. While historical surveys in Australia have indicated that Ae. aegypti occurred over much of the continent, its range has receded from Western Australia, the Northern Territory and New South Wales (NSW) over the last 50 years. It is now only found in Queensland, although recent incursions into the Northern Territory have required costly eradication strategies. The significant reduction in vector distribution has been attributed to a combination of events including the introduction of reticulated water, which reduced the domestic water storage requirements of households that had provided stable larval sites, as well as the removal of the railway-based water storage containers hypothesised as being responsible for the long distance dispersal.

“Drought-proofing” Australia’s urban regions by installing large domestic water tanks may enable the dengue mosquito Ae. aegypti to regain its foothold across the country and expand its range of possible infections. A new paper challenges the common assumption that climate change will drive the spread of this mosquito, suggesting instead that the real driver is human behavior. The study combines current and forecasted climate change conditions with historical epidemics to reveal the risk of dengue infections in all capital cities around Australia by 2050. Researchers developed and critically assessed their models to project the distribution of the mosquito in 2030 and 2050. Currently, dengue fever occurs in Queensland only. However, the implementation of new water tanks, combined with already warm summer temperatures, could enable the mosquito to re-emerge and further its current reach. Dengue risks will not be driven directly by warmer temperatures or changes in rainfall patterns. Australian summers already provide ideal conditions for dengue transmission around the country, but the introduction of government-subsidized water storage devices now adds the ideal breeding ground for the dengue mosquito to re-emerge. While research is properly focused on the impact of anthropogenic climate change, this study highlights the need to look also at our responses to those changes and the outcomes they generate. The current dengue fever epidemic in far north Queensland is approaching 1,000 reported cases over the summer of 2008-2009.

Australia’s Dengue Risk Driven by Human Adaptation to Climate Change. 2009 PLoS Negl Trop Dis 3(5): e429
The reduced rainfall in southeast Australia has placed this region’s urban and rural communities on escalating water restrictions, with anthropogenic climate change forecasts suggesting that this drying trend will continue. To mitigate the stress this may place on domestic water supply, governments have encouraged the installation of large domestic water tanks in towns and cities throughout this region. These prospective stable mosquito larval sites create the possibility of the reintroduction of Ae. aegypti from Queensland, where it remains endemic, back into New South Wales and other populated centres in Australia, along with the associated emerging and re-emerging dengue risk if the virus was to be introduced. Having collated the known distribution of Ae. aegypti in Australia, we built distributional models using a genetic algorithm to project Ae. aegypti’s distribution under today’s climate and under climate change scenarios for 2030 and 2050 and compared the outputs to published theoretical temperature limits. Incongruence identified between the models and theoretical temperature limits highlighted the difficulty of using point occurrence data to study a species whose distribution is mediated more by human activity than by climate. Synthesis of this data with dengue transmission climate limits in Australia derived from historical dengue epidemics suggested that a proliferation of domestic water storage tanks in Australia could result in another range expansion of Ae. aegypti which would present a risk of dengue transmission in most major cities during their warm summer months. In the debate of the role climate change will play in the future range of dengue in Australia, we conclude that the increased risk of an Ae. aegypti range expansion in Australia would be due not directly to climate change but rather to human adaptation to the current and forecasted regional drying through the installation of large domestic water storing containers. The expansion of this efficient dengue vector presents both an emerging and re-emerging disease risk to Australia. Therefore, if the installation and maintenance of domestic water storage tanks is not tightly controlled, Ae. aegypti could expand its range again and cohabit with the majority of Australia’s population, presenting a high potential dengue transmission risk during warm summers.

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Geostatistical maps are increasingly being used to plan neglected tropical disease control programmes. A decade after the conclusion of a schistosomiasis control program in Mali, prevalence of the disease has regressed to pre-intervention levels. New research finds that clusters of schistosomiasis infections occur generally in the same areas ten years after the end of a donor-funded control program, conducted between 1982 and 1992.

Schistosomiasis is a parasitic disease caused by several species of fluke of the genus Schistosoma. Although it has a low mortality rate, schistosomiasis often is a chronic illness that can damage internal organs and, in children, impair growth and cognitive development. Mali is one of the first countries in sub-Saharan Africa to have initiated a national schistosomiasis control program. Lack of government funding curtailed the program’s activities after 1998, until a new program, backed by the Schistosomiasis Control Initiative, began in 2004.

The authors undertook a comparative study of the spatial distribution of schistosomiasis in Mali between 1984-1989 and 2004-2006. They show that the spatial distribution of schistosomiasis was similar in both time periods, even in the face of large-scale control program based on mass distribution of anti-parasitic drugs. Long-term stability in the spatial distribution of schistosomiasis means that reviewing historic data can provide a useful, initial source of evidence for planning targeted contemporary control program. However, if these control program are to have a sustainable impact on the burden of schistosomiasis they must be delivered over a very long time period, or supplementary methods need to be implemented, such as improvement in water sanitation and hygiene.

This work has two main implications: that historic data can be used, in the first instance, to plan contemporary control programmes due to the stability of the spatial distribution of schistosomiasis; and that a decade of donor-funded mass distribution of praziquantel has had no discernable impact on the burden of schistosomiasis in subsequent generations of Malians, probably due to rapid reinfection.

A Comparative Study of the Spatial Distribution of Schistosomiasis in Mali in 1984–1989 and 2004–2006. 2009 PLoS Negl Trop Dis 3(5): e431
We investigated changes in the spatial distribution of schistosomiasis in Mali following a decade of donorfunded control and a further 12 years without control. National pre-intervention cross-sectional schistosomiasis surveys were conducted in Mali in 1984–1989 (in communities) and again in 2004–2006 (in schools). Bayesian geostatistical models were built separately for each time period and on the datasets combined across time periods. In the former, data from one period were used to predict prevalence of schistosome infections for the other period, and in the latter, the models were used to determine whether spatial autocorrelation and covariate effects were consistent across periods. Schistosoma haematobium prevalence was 25.7% in 1984–1989 and 38.3% in 2004–2006; S. mansoni prevalence was 7.4% in 1984–1989 and 6.7% in 2004–2006 (note the models showed no significant difference in mean prevalence of either infection between time periods). Prevalence of both infections showed a focal spatial pattern and negative associations with distance from perennial waterbodies, which was consistent across time periods. Spatial models developed using 1984–1989 data were able to predict the distributions of both schistosome species in 2004–2006 (area under the receiver operating characteristic curve was typically >0.7) and vice versa. A decade after the apparently successful conclusion of a donor-funded schistosomiasis control programme from 1982–1992, national prevalence of schistosomiasis had rebounded to pre-intervention levels. Clusters of schistosome infections occurred in generally the same areas accross time periods, although the precise locations varied. To achieve long-term control, it is essential to plan for sustainability of ongoing interventions, including stengthening endemic country health systems.

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A paper published in this week’s issue of PLoS Biology describes a study that has reactivated a dormant gene found in humans and coaxed it – in tissue culture – to produce an antiviral peptide. Lead scientist Alexander Cole used aminoglycosides – drugs commonly used to fight bacterial infections – to trigger the production of the protein, which is encoded by the dormant human defensin gene that he calls “retrocyclin”. The authors hope that this research might ultimately lead to the development of a treatment that would activate the gene in a person’s own cells, for example, and thereby prevent infection with viruses in the treated tissue.

Defensins are a large family of small antimicrobial peptides that contribute to host defense against a broad spectrum of pathogens. In primates, defensins are divided into three subfamilies – alpha, beta, and theta – on the basis of their disulfide bonding pattern. Theta-defensins were the most recently identified defensin subfamily, isolated initially from white blood cells and bone marrow of rhesus monkeys. They are the only known cyclic peptides in mammals and act primarily by preventing viruses such as HIV-1 from entering cells. Whereas theta-defensin genes are intact in Old World monkeys, in humans they have a premature stop codon that prevents their expression; they thus exist as pseudogenes. On correction of the premature termination codon in theta-defensin pseudogenes, human myeloid cells produce cyclic, antiviral peptides, indicating that the cells retain the intact machinery to make cyclic peptides. Given that the endogenous production of retrocyclins could also be restored in human tissues, the possibility exists that that aminoglycoside-based topical microbicides might be useful in preventing sexual transmission of HIV-1.

Dozens of scientists around the world are looking for ways to prevent the transmission of viruses such as HIV. Cole and colleagues have previously discovered that retrocyclin proteins found in some primates appeared to prevent HIV infections in cell cultures. The same gene exists in humans, but because of a mutation that interrupts the gene sequence, it no longer produces protein. Now, a collaboration between researchers has found that restoring the production of retrocyclins prevents HIV entry into human cells. The scientists have found a way to get the gene to produce the retrocyclin and then showed that the retrocyclin appears to prevent the transmission of HIV in cells cultured in the laboratory. They applied aminoglycoside antibiotics to vaginal tissues and cervical cells in the lab and found the antibiotic appears to stimulate those cells and tissues to produce retrocyclins on their own. There is a possibility the aminoglycoside antibiotics will be used in a cream or gel format that could someday be a simple way to prevent the transmission of HIV. Much more work would be required before this would be possible, including taking the result in tissue culture and showing the same effect in whole organisms.

Reawakening retrocyclins: ancestral human defensins active against HIV-1. 2009 PLoS Biol 7(4):e1000095
Human alpha and beta defensins contribute substantially to innate immune defenses against microbial and viral infections. Certain nonhuman primates also produce theta-defensins—18 residue cyclic peptides that act as HIV-1 entry inhibitors. Multiple human theta-defensin genes exist, but they harbor a premature termination codon that blocks translation. Consequently, the theta-defensins (retrocyclins) encoded within the human genome are not expressed as peptides. In vivo production of theta-defensins in rhesus macaques involves the post-translational ligation of two nonapeptides, each derived from a 12-residue ‘‘demidefensin’’ precursor. Neither the mechanism of this unique process nor its existence in human cells is known. To ascertain if human cells retained the ability to process demidefensins, we transfected human promyelocytic cells with plasmids containing repaired retrocyclin-like genes. The expected peptides were isolated, their sequences were verified by mass spectrometric analyses, and their anti-HIV-1 activity was confirmed in vitro. Our study reveals for the first time, to our knowledge, that human cells have the ability to make cyclic theta-defensins. Given this evidence that human cells could make theta-defensins, we attempted to restore endogenous expression of retrocyclin peptides. Since human theta-defensin genes are transcribed, we used aminoglycosides to read-through the premature termination codon found in the mRNA transcripts. This treatment induced the production of intact, bioactive retrocyclin-1 peptide by human epithelial cells and cervicovaginal tissues. The ability to reawaken retrocyclin genes from their 7 million years of slumber using aminoglycosides could provide a novel way to secure enhanced resistance to HIV-1 infection.

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