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The transmission spectra of exoplanet atmospheres observed with the Hubble Space Telescope (HST) in the near-infrared range (1.1-1.65$\mu$m) frequently show evidence for some combination of clouds and hazes. Identification of systematic trends in exoplanet clouds and hazes is potentially important for understanding atmospheric composition and temperature structure. Here we report on the analysis of spectral modulation using a large, uniformly processed sample of HST/WFC3 transit spectra from 62 exoplanets. The spectral retrieval includes the capability to detect and represent atmospheres in which the composition departs from thermochemical equilibrium. By using this unique catalog and measuring the dampening of spectral modulations compared to strictly clear atmospheres, we identify two populations. One is completely cloud/haze free spanning a wide temperature range, while the other population, identified as ``Partial cloud/hazes'', follows a trend from mostly cloudy/hazy around 500~K to mostly clear at $\sim$1500~K. We also find that a partially transparent aerosol component is frequently present and that it is typically vertically distributed throughout the atmospheric column. Our findings also suggest that while clouds and hazes are common in exoplanet atmospheres, the majority of planets have some level of detectable spectral modulation. Additionally, the empirical trend that clouds and hazes are minimized at 1460.86K$^{+316}_{-405}$ revealed in our catalog has predictive utility for modelling the performance of large-scale transiting exoplanets survey, such as planned with the Ariel mission. This trend can also be used for making a probability-based forecast of spectral modulation for a given source in the context of future JWST observations. Future observations including the optical and/or a broader spectral coverage may be useful to further quantify the trend reported here., Comment: 12 pages, 4 figures, accepted for publication in ApjL

The formation of hazes at microbar pressures has been explored by theoretical models of exoplanet atmospheres to explain Rayleigh scattering and/or featureless transmission spectra; however observational evidence of aerosols in the low-pressure formation environments has proved elusive. Here, we show direct evidence of aerosols existing at ∼1 microbar pressures in the atmosphere of the warm sub-Saturn WASP-69b using observations taken with the Space Telescope Imaging Spectrograph and Wide Field Camera 3 instruments on the Hubble Space Telescope. The transmission spectrum shows a wavelength-dependent slope induced by aerosol scattering that covers 11 scale heights of spectral modulation. Drawing on the extensive studies of haze in our solar system, we model the transmission spectrum based on a scaled version of Jupiter's haze-density profile to show that the WASP-69b transmission spectrum can be produced by scattering from an approximately constant density of particles extending throughout the atmospheric column from 40 millibar to microbar pressures. These results are consistent with theoretical expectations based on microphysics of the aerosol particles that have suggested haze can exist at microbar pressures in exoplanet atmospheres. © 2021. The American Astronomical Society. All rights reserved., This research has made use of the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. R.E. and M.S. acknowledge support for a portion of this effort from NASA ADAP award 907524. R.E. acknowledges the Sao Paulo Research Foundation for the fellowship #2018/09984-7. This work has been supported in part by the California Institute of Technology Jet Propulsion Laboratory Exoplanet Science Initiative. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004; 2021). All rights reserved., With funding from the Spanish government through the Severo Ochoa Centre of Excellence accreditation SEV-2017-0709.

The discovery of potentially habitable planets around the ultracool dwarf star Trappist-1 naturally poses the question: could Trappist-1 planets be home to life? These planets orbit very close to the host star and are most susceptible to the UV radiation emitted by the intense and frequent flares of Trappist-1. Here we calculate the UV spectra (100 - 450 nm) of a superflare observed on Trappist-1 with the K2 mission. We couple radiative transfer models to this spectra to estimate the UV surface flux on planets in the habitable zone of Trappist-1 (planets $e$, $f$, and $g$), assuming atmospheric scenarios based on a pre-biotic and an oxygenic atmosphere. We quantify the impact of the UV radiation on living organisms on the surface and on a hypothetical planet ocean. Finally, we find that for non-oxygenic planets, UV resistant lifeforms would survive on the surface of planets f and g. Nevertheless, more fragile organisms (i.e. \textit{E. coli}) could be protected from the hazardous UV effects at ocean depths greater than 8m. If the planets have an ozone layer, any lifeforms studied here would survive in the HZ planets., 13 pages, 6 figures, accepted for publication in Astrobiology

We report the detection of an atmosphere on a rocky exoplanet, GJ 1132 b, which is similar to Earth in terms of size and density. The atmospheric transmission spectrum was detected using Hubble WFC3 measurements and shows spectral signatures of aerosol scattering, HCN, and CH$_{4}$ in a low mean molecular weight atmosphere. We model the atmospheric loss process and conclude that GJ 1132 b likely lost the original H/He envelope, suggesting that the atmosphere that we detect has been reestablished. We explore the possibility of H$_{2}$ mantle degassing, previously identified as a possibility for this planet by theoretical studies, and find that outgassing from ultrareduced magma could produce the observed atmosphere. In this way we use the observed exoplanet transmission spectrum to gain insights into magma composition for a terrestrial planet. The detection of an atmosphere on this rocky planet raises the possibility that the numerous powerfully irradiated Super-Earth planets, believed to be the evaporated cores of Sub-Neptunes, may, under favorable circumstances, host detectable atmospheres., 22 pages, 12 figures, accepted for publication in Astronomical Journal

Observations of various solar-type stars along decades revealed that they can have magnetic cycles, just like our Sun. An investigation of the relation between their cycle length and rotation period can shed light on the dynamo mechanisms operating in these stars. Previous works on this relation suggested that the stars could be separated into active and inactive branches, with the Sun falling between them. In this work, we determined short magnetic activity cycles for 6 active solar-type stars observed by the Kepler telescope. The method adopted here estimates the activity from the excess in the residuals of the transitlight curves. This excess is obtained by subtracting a spotless model transit from the light curve, and then integrating over all the residuals during the transit. The presence of long term periodicity is estimated from the analysis of a Lomb-Scargle periodogram of the complete time series. Finally, we investigate the rotation-cycle period relation for the stars analysed here and find that some active stars do not follow the behaviour proposed earlier, falling in the inactive branch. In addition, we also notice a considerable spread from other stars in the literature in the active/inactive branches., 8 pages, 4 figures, Proceedings of the IAU Symposium No. 328: "Living Around Active Stars"

The production of bioenergy from plant biomass previously relied on using microorganisms that rapidly and efficiently convert simple sugars into fuels and chemicals. However, to exploit the far more abundant carbon fixed in plant cell walls, future industrial production hosts will need to be engineered to leverage the most efficient biochemical pathways and most robust traits that can be found in nature. The CRISPR-Cas9 genome editing technology now enables writing the genome at will, which will allow biotechnology to become an 'information science.' This review covers recent advances in using CRISPR-Cas9 to engineer the genomes of a wide variety of organisms that could be use in the industrial production of biofuels and renewable chemicals.

Economical biofuel production from plant biomass requires the conversion of both cellulose and hemicellulose in the plant cell wall. The best industrial fermentation organism, the yeast Saccharomyces cerevisiae, has been developed to utilize xylose by heterologously expressing either a xylose reductase/xylitol dehydrogenase (XR/XDH) pathway or a xylose isomerase (XI) pathway. Although it has been proposed that the optimal means for fermenting xylose into biofuels would use XI instead of the XR/XDH pathway, no clear comparison of the best publicly-available yeast strains engineered to use XR/XDH or XI has been published. We therefore compared two of the best-performing engineered yeast strains in the public domain—one using the XR/XDH pathway and another using XI—in anaerobic xylose fermentations. We find that, regardless of conditions, the strain using XR/XDH has substantially higher productivity compared to the XI strain. By contrast, the XI strain has better yields in nearly all conditions tested.

Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits—thermotolerance, lipid production, and facile transformation with exogenous DNA—into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals. IMPORTANCE The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications. Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications.

The potentially important role of stellar irradiation in envelope removal for planets with diameters of $\lessapprox$ 2 R$_{\Earth}$ has been inferred both through theoretical work and the observed bimodal distribution of small planet occurrence as a function of radius. We examined the trends for small planets in the three-dimensional radius-insolation-density space and find that the terrestrial planets divide into two distinct families based on insolation. The lower insolation family merges with terrestrial planets and small bodies in the solar system and is thus Earth-like. The higher insolation terrestrial planet family forms a bulk-density continuum with the sub-Neptunes, and is thus likely to be composed of remnant cores produced by photoevaporation. Based on the density-radius relationships, we suggest that both terrestrial families show evidence of density enhancement through collisions. Our findings highlight the important role that both photoevaporation and collisions have in determining the density of small planets., Comment: 9 pages, 6 figures, Accepted for publication in ApJ

Kepler-96 is an active solar-type star harbouring a Super-Earth planet in close orbit. Its age of 2.3 Gyr is the same as the Sun when there was a considerable increase of oxygen in Earth's atmosphere due to micro-organisms living in the ocean. We present the analysis of superflares seen on the transit lightcurves of Kepler-96b. The model used here simulates the planetary transit in a flaring star. By fitting the observational data with this model, it is possible to infer the physical properties of the flares, such as their duration and the energy released. We found 3 flares within the energy range of superflares, where the biggest superflare observed was found to have an energy of 1.81$\times$10$^{35}$ ergs. The goal is to analyse the biological impact of these superflares on a hypothetical Earth in the habitable zone of Kepler-96 assuming this planet has protection via different scenarios: an Archean and Present-day atmospheres. Also, we compute the attenuation of the flare UV radiation through an Archean ocean. The conclusion is that considering the increase in the UV flux by the strongest superflare emission, {\it E. Coli} and {\it D. Radiodurans} could survive on the surface of the planet only if there was an ozone layer present on the planet atmosphere. However, they could escape from the hazardous UV effects at a depth of 28m and 12m below the ocean surface, respectively. For smaller superflares contribution, {\it D. Radiodurans} could survive in the surface even in an Archean atmosphere with no ozone., 22 pages, 9 figures, accepted for publication in Astrobiology

Magnetic activity on stars manifests itself in the form of dark spots on the stellar surface, that cause modulation of a few percent in the light curve of the star as it rotates. When a planet eclipses its host star, it might cross in front of one of these spots creating a "bump" in the transit light curve. By modelling these spot signatures, it is possible to determine the physical properties of the spots such as size, temperature, and location. In turn, the monitoring of the spots longitude provides estimates of the stellar rotation and differential rotation. This technique was applied to the star Kepler-17, a solar--type star orbited by a hot Jupiter. The model yields the following spot characteristics: average radius of $49 \pm 10$ Mm, temperatures of $5100 \pm 300$ K, and surface area coverage of $6 \pm 4$ \%. The rotation period at the transit latitude, $-5^\circ$, occulted by the planet was found to be $11.92 \pm 0.05$ d, slightly smaller than the out--of--transit average period of $12.4 \pm 0.1$ d. Adopting a solar like differential rotation, we estimated the differential rotation of Kepler-17 to be $\Delta\Omega = 0.041 \pm 0.005$ rd/d, which is close to the solar value of 0.050 rd/d, and a relative differential rotation of $\Delta\Omega/\Omega=8.0 \pm 0.9$ \%. Since Kepler-17 is much more active than our Sun, it appears that for this star larger rotation rate is more effective in the generation of magnetic fields than shear., Comment: 9 pages, 11 figures, published in ApJ

The stellar magnetic field plays a crucial role in the star internal mechanisms, as in the interactions with its environment. The study of starspots provides information about the stellar magnetic field, and can characterise the cycle. Moreover, the analysis of solar-type stars is also useful to shed light onto the origin of the solar magnetic field. The objective of this work is to characterise the magnetic activity of stars. Here, we studied two solar-type stars Kepler-17 and Kepler-63 using two methods to estimate the magnetic cycle length. The first one characterises the spots (radius, intensity, and location) by fitting the small variations in the light curve of a star caused by the occultation of a spot during a planetary transit. This approach yields the number of spots present in the stellar surface and the flux deficit subtracted from the star by their presence during each transit. The second method estimates the activity from the excess in the residuals of the transit lightcurves. This excess is obtained by subtracting a spotless model transit from the lightcurve, and then integrating all the residuals during the transit. The presence of long term periodicity is estimated in both time series. With the first method, we obtained $P_{\rm cycle}$ = 1.12 $\pm$ 0.16 yr (Kepler-17) and $P_{\rm cycle}$ = 1.27 $\pm$ 0.16 yr (Kepler-63), and for the second approach the values are 1.35 $\pm$ 0.27 yr and 1.27 $\pm$ 0.12 yr, respectively. The results of both methods agree with each other and confirm their robustness., Comment: Accepted for publication in ApJ. 18 pages, 27 figures

Graphical abstract, Highlights • Publicly available xylose-fermenting Saccharomyces cerevisiae were compared. • Yeast using xylose reductase/xylitol dehydrogenase had higher ethanol production. • Yeast using xylose isomerase had better ethanol yields from xylose. • Yeast using xylose reductase/xylitol dehydrogenase finish fermentations faster. • Comparisons between the two strains provide benchmarks for future engineering., Economical biofuel production from plant biomass requires the conversion of both cellulose and hemicellulose in the plant cell wall. The best industrial fermentation organism, the yeast Saccharomyces cerevisiae, has been developed to utilize xylose by heterologously expressing either a xylose reductase/xylitol dehydrogenase (XR/XDH) pathway or a xylose isomerase (XI) pathway. Although it has been proposed that the optimal means for fermenting xylose into biofuels would use XI instead of the XR/XDH pathway, no clear comparison of the best publicly-available yeast strains engineered to use XR/XDH or XI has been published. We therefore compared two of the best-performing engineered yeast strains in the public domain—one using the XR/XDH pathway and another using XI—in anaerobic xylose fermentations. We find that, regardless of conditions, the strain using XR/XDH has substantially higher productivity compared to the XI strain. By contrast, the XI strain has better yields in nearly all conditions tested.

Sustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungus Neurospora crassa as a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Reconstitution of this xylodextrin utilization pathway in Saccharomyces cerevisiae revealed that fungal xylose reductases act as xylodextrin reductases, producing xylosyl-xylitol oligomers as metabolic intermediates. These xylosyl-xylitol intermediates are generated by diverse fungi and bacteria, indicating that xylodextrin reduction is widespread in nature. Xylodextrins and xylosyl-xylitol oligomers are then hydrolyzed by two hydrolases to generate intracellular xylose and xylitol. Xylodextrin consumption using a xylodextrin transporter, xylodextrin reductases and tandem intracellular hydrolases in cofermentations with sucrose and glucose greatly expands the capacity of yeast to use plant cell wall-derived sugars and has the potential to increase the efficiency of both first-generation and next-generation biofuel production. DOI: http://dx.doi.org/10.7554/eLife.05896.001, eLife digest Plants can be used to make ‘biofuels’, which are more sustainable alternatives to traditional fuels made from petroleum. Unfortunately, most biofuels are currently made from simple sugars or starch extracted from parts of plants that we also use for food, such as the grains of cereal crops. Making biofuels from the parts of the plant that are not used for food—for example, the stems or leaves—would enable us to avoid a trade-off between food and fuel production. However, most of the sugars in these parts of the plant are locked away in the form of large, complex carbohydrates called cellulose and hemicellulose, which form the rigid cell wall surrounding each plant cell. Currently, the industrial processes that can be used to make biofuels from plant cell walls are expensive and use a lot of energy. They involve heating or chemically treating the plant material to release the cellulose and hemicellulose. Then, large quantities of enzymes are added to break these carbohydrates down into simple sugars that can then be converted into alcohol (a biofuel) by yeast. Fungi may be able to provide us with a better solution. Many species are able to grow on plants because they can break down cellulose and hemicellulose into simple sugars they can use for energy. If the genes involved in this process could be identified and inserted into yeast it may provide a new, cheaper method to make biofuels from plant cell walls. To address this challenge, Li et al. studied how the fungus Neurospora crassa breaks down hemicellulose. This study identified a protein that can transport molecules of xylodextrin—which is found in hemicellulose—into the cells of the fungus, and two enzymes that break down the xylodextrin to make simple sugars, using a previously unknown chemical intermediate. When Li et al. inserted the genes that make the transport protein and the enzymes into yeast, the yeast were able to use plant cell wall material to make simple sugars and convert these to alcohol. The yeast used more of the xylodextrin when they were grown with an additional source of energy, such as the sugars glucose or sucrose. Li et al.'s findings suggest that giving yeast the ability to break down hemicellulose has the potential to improve the efficiency of biofuel production. The next challenge will be to improve the process so that the yeast can convert the xylodextrin and simple sugars more rapidly. DOI: http://dx.doi.org/10.7554/eLife.05896.002

Sustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungusNeurospora crassaas a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Successful reconstitution of this xylodextrin utilization pathway inSaccharomyces cerevisiaerevealed that fungal xylose reductases act as xylodextrin reductases, and together with two hydrolases, generate intracellular xylose and xylitol. Xylodextrin consumption using xylodextrin reductases and tandem intracellular hydrolases greatly expands the capacity of yeasts to use plant cell wall-derived sugars, and should be adaptable to increase the efficiency of both first-generation and next-generation biofuel production.

Aims. The wavelet transform has been used as a powerful tool for treating several problems in astrophysics. In this work, we show that the time-frequency analysis of stellar light curves using the wavelet transform is a practical tool for identifying rotation, magnetic activity, and pulsation signatures. We present the wavelet spectral composition and multiscale variations of the time series for four classes of stars: targets dominated by magnetic activity, stars with transiting planets, those with binary transits, and pulsating stars. Methods. We applied the Morlet wavelet (6th order), which offers high time and frequency resolution. By applying the wavelet transform to the signal, we obtain the wavelet local and global power spectra. The first is interpreted as energy distribution of the signal in time-frequency space, and the second is obtained by time integration of the local map. Results. Since the wavelet transform is a useful mathematical tool for nonstationary signals, this technique applied to Kepler and CoRoT light curves allows us to clearly identify particular signatures for different phenomena. In particular, patterns were identified for the temporal evolution of the rotation period and other periodicity due to active regions affecting these light curves. In addition, a beat-pattern signature in the local wavelet map of pulsating stars over the entire time span was also detected., Comment: Accepted for publication on A&A

Orientadores: Gonçalo Amarante Guimarães Pereira, Laudiene Evangelista Meyer Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A necessidade do desenvolvimento de alternativas energéticas renováveis, limpas e de baixo custo, capazes de substituir o "petrodiesel" sem impactar a produção de alimentos, é a principal motivação para o desenvolvimento do projeto. Entre as alternativas, o cultivo de microalgas tem sido recorrentemente relatado como muito promissor. Microalgas são espécies unicelulares fotossintetizantes capazes de acumular lipídeos naturalmente. Entretanto, ainda não há cepas desenvolvidas para o uso industrial, havendo diversas barreiras tecnológicas a serem vencidas, como os altos custos de implantação e a dificuldade de encontrar organismos que aliem velocidade de crescimento e boa produtividade lipídica. Para o desenvolvimento do projeto selecionamos a espécie de microalga Neochloris oleoabundans devido à sua capacidade naturalmente superior em acumular lipídeos. O principal objetivo foi identificar estímulos ambientais capazes de induzir maior produção e acúmulo de cadeias carbônicas lipídicas nessa espécie e, então, iniciar análises moleculares nessas situações. Os primeiros cultivos de N. oleoabundans caracterizaram-se pelo crescimento muito lento nos diversos meios autotróficos testados, porém, ao final do projeto, percebemos que os cultivos cresciam com velocidade muito superior às culturas iniciais. Ao compilar os dados de crescimento obtidos nesses dois anos, vimos que as taxas de duplicação de N. oleoabundans foram elevadas em cerca de seis vezes nesse período. Acreditamos que houve seleção artificial de células mais velozes à medida que repicávamos os cultivos a fim de iniciar culturas novas. Para identificar condições capazes de induzir maior acúmulo lipídico, N. oleoabundans foi submetida a situações de estresse como privação de fósforo e nitrogênio. Observamos que a privação de nitrogênio foi capaz de desencadear aumento de teor lipídico muito expressivo. Então, sequenciamos o genoma e averiguamos a expressão gênica de algumas enzimas da via de biossíntese de ácidos graxos em privação de nitrogênio. Observamos também que cultivos feitos em meio heterotrófico mostravam-se rapidamente contaminados. A montagem do genoma pode dar indícios da natureza dessa contaminação recorrente, pois foram encontradas sequências de uma bactéria do gênero Brevundimonas. Ao investigar esse contaminante vimos que o mesmo pode estar em simbiose com a microalga, há relatos na literatura sobre simbioses dessa natureza, onde o procarioto fornece vitamina B12 e a microalga, matéria orgânica para o crescimento do mesmo. Encontramos enzimas dependentes dessa vitamina como cofator no genoma de N. oleoabundans, indicando que pode haver uma simbiose entre esses organismos. Devido aos bons resultados obtidos acreditamos que o estudo e manipulação a nível molecular dessa espécie podem torná-la potencialmente aplicável na indústria. O entendimento do mecanismo molecular de acúmulo lipídico sobre estresse, aliado ao potencial de seleção artificial de cepas velozes revelado, permite gerar conhecimento suficiente para agrupar em uma única espécie rápido crescimento e teor lipídico elevado Abstract: Coal, petroleum and natural gas are cheap and may not run out soon. However, considering political and environmental implications associated with them, there appears to be no net economic benefit in its use. Therefore, sustainable alternatives are really necessary due to the global growing demand of energy. Among the alternatives, cultivation of microalgae has been reported as a promising technology. Algae use sunlight to produce biochemical energy via photosynthesis and its oil productivity and growth rates greatly exceeds that of vascular plants. Unlike the existing crop-derived biofuels, algae fuels can be produced without encroaching on food cropland. The technology is being intensively investigated by nearly every major and startups oil companies nowadays. However, there are no species developed for industrial use and there are several technological barriers to overcome. In this study we investigated the microalga Neochloris oleoabundans, selected for its naturally higher ability to accumulate lipids. Initially, N. oleoabundans growth rates were very low. We decreased by six times the cell doubling time, we believe that occurred artificial selection of faster growing cells during the master's period. Nitrogen starvation led to great increases in cellular lipid content. Real-time PCR experiments show that some key enzymes of fatty acid biosynthesis are differentially expressed in nitrogen starved cultures. The genome of N. oleoabundans was sequenced using Solexa® technology and preliminary analysis show the presence of a bacterium associated with the microalga. We believe that there is a symbiotic relationship between them, since the alga needs vitamin B12 despite being not capable of producing it. Our analysis show that N. oleoabundans is a very promising strain. The excellent response to nitrogen starvation and knowledge acquired with genomic approach led us to a better understanding of N. oleoabundans metabolism, indicating that this specie may be suitable for industrial application Mestrado Genética de Microorganismos Mestre em Genética e Biologia Molecular

Background The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches' Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. M. perniciosa, together with the related species M. roreri, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of M. perniciosa was analyzed to evaluate the overall gene content of this phytopathogen. Results Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that M. perniciosa has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that M. perniciosa have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in M. perniciosa genome survey. Conclusion This genome survey gives an overview of the M. perniciosa genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the M. perniciosa/cacao pathosystem.

Background Saccharomyces cerevisiae, a key organism used for the manufacture of renewable fuels and chemicals, has been engineered to utilize non-native sugars derived from plant cell walls, such as cellobiose and xylose. However, the rates and efficiencies of these non-native sugar fermentations pale in comparison with those of glucose. Systems biology methods, used to understand biological networks, hold promise for rational microbial strain development in metabolic engineering. Here, we present a systematic strategy for optimizing non-native sugar fermentation by recombinant S. cerevisiae, using cellobiose as a model. Results Differences in gene expression between cellobiose and glucose metabolism revealed by RNA deep sequencing indicated that cellobiose metabolism induces mitochondrial activation and reduces amino acid biosynthesis under fermentation conditions. Furthermore, glucose-sensing and signaling pathways and their target genes, including the cAMP-dependent protein kinase A pathway controlling the majority of glucose-induced changes, the Snf3-Rgt2-Rgt1 pathway regulating hexose transport, and the Snf1-Mig1 glucose repression pathway, were at most only partially activated under cellobiose conditions. To separate correlations from causative effects, the expression levels of 19 transcription factors perturbed under cellobiose conditions were modulated, and the three strongest promoters under cellobiose conditions were applied to fine-tune expression of the heterologous cellobiose-utilizing pathway. Of the changes in these 19 transcription factors, only overexpression of SUT1 or deletion of HAP4 consistently improved cellobiose fermentation. SUT1 overexpression and HAP4 deletion were not synergistic, suggesting that SUT1 and HAP4 may regulate overlapping genes important for improved cellobiose fermentation. Transcription factor modulation coupled with rational tuning of the cellobiose consumption pathway significantly improved cellobiose fermentation. Conclusions We used systems-level input to reveal the regulatory mechanisms underlying suboptimal metabolism of the non-glucose sugar cellobiose. By identifying key transcription factors that cause suboptimal cellobiose fermentation in engineered S. cerevisiae, and by fine-tuning the expression of a heterologous cellobiose consumption pathway, we were able to greatly improve cellobiose fermentation by engineered S. cerevisiae. Our results demonstrate a powerful strategy for applying systems biology methods to rapidly identify metabolic engineering targets and overcome bottlenecks in performance of engineered strains. Electronic supplementary material The online version of this article (doi:10.1186/s13068-014-0126-6) contains supplementary material, which is available to authorized users.