Artificial intelligence yields new antibiotic

A deep-learning model identifies a powerful new drug that can kill many species of antibiotic-resistant bacteria

Using a machine-learning algorithm, researchers have identified a powerful new antibiotic compound. In laboratory tests, the drug killed many of the world's most problematic disease-causing bacteria, including some strains that are resistant to all known antibiotics. It also cleared infections in two different mouse models.

Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep neural network capable of predicting molecules with antibacterial activity. We performed predictions on multiple chemical libraries and discovered a molecule from the Drug Repurposing Hub—halicin—that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens including Mycobacterium tuberculosis and carbapenem-resistant Enterobacteriaceae. Halicin also effectively treated Clostridioides difficile and pan-resistant Acinetobacter baumannii infections in murine models. Additionally, from a discrete set of 23 empirically tested predictions from >107 million molecules curated from the ZINC15 database, our model identified eight antibacterial compounds that are structurally distant from known antibiotics. This work highlights the utility of deep learning approaches to expand our antibiotic arsenal through the discovery of structurally distinct antibacterial molecules.


Journal Reference: Jonathan M. Stokes, Kevin Yang, Kyle Swanson, Wengong Jin, Andres Cubillos-Ruiz, Nina M. Donghia, Craig R. MacNair, Shawn French, Lindsey A. Carfrae, Zohar Bloom-Ackerman, Victoria M. Tran, Anush Chiappino-Pepe, Ahmed H. Badran, Ian W. Andrews, Emma J. Chory, George M. Church, Eric D. Brown, Tommi S. Jaakkola, Regina Barzilay, James J. Collins. A Deep Learning Approach to Antibiotic Discovery. Cell, 2020; 180 (4): 688 DOI: 10.1016/j.cell.2020.01.021

Alcohol-producing gut bacteria could cause liver damage even in people who don't drink

Summary: Non-alcoholic fatty liver disease (NAFLD) is the build-up of fat in the liver due to factors other than alcohol, but its cause remains unknown. Now, researchers have linked NAFLD to gut bacteria that produce a large amount of alcohol in the body, finding these bacteria in over 60% of NAFLD patients. 

Their findings could help develop a screening method for early diagnosis and treatment of non-alcoholic fatty liver.

Because K. pneumonia produce alcohol using sugar, patients who carry these bacteria would have a detectable amount of alcohol in their blood after drinking a simple glucose solution. "In the early stages, fatty liver disease is reversible. If we can identify the cause sooner, we could treat and even prevent liver damage."

"Having these bacteria in your gut means your body is exposed to alcohol constantly," Liu says. "So does being a carrier mean you would have higher alcohol tolerance? I'm genuinely curious!"

Journal Reference: Jing Yuan, Chen Chen, Jinghua Cui, Jing Lu, Chao Yan, Xiao Wei, Xiangna Zhao, NanNan Li, Shaoli Li, Guanhua Xue, Weiwei Cheng, Boxing Li, Huan Li, Weishi Lin, Changyu Tian, Jiangtao Zhao, Juqiang Han, Daizhi An, Qiong Zhang, Hong Wei, Minghua Zheng, Xuejun Ma, Wei Li, Xiao Chen, Zheng Zhang, Hui Zeng, Sun Ying, JianXin Wu, Ruifu Yang, Di Liu. Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae. Cell Metabolism, 2019; DOI: 10.1016/j.cmet.2019.08.018

Effects of Microplastics in Soil Ecosystems: Above and Below Ground

Abstract: Environmental contamination by microplastics is now considered an emerging threat to biodiversity and ecosystem functioning. Soil ecosystems, particularly agricultural land, have been recognized as a major sink of microplastics, but the impacts of microplastics on soil ecosystems (e.g., above and below ground) remain largely unknown.

In this study, different types of microplastics [biodegradable polylactic acid (PLA)], conventional high-density polyethylene (HDPE), and microplastic clothing fibers were added to soil containing the endogeic Aporrectodea rosea (rosy-tipped earthworm) and planted with Lolium perenne (perennial ryegrass) to assess the biophysical soil response in a mesocosm experiment. When exposed to fibers or PLA microplastics, fewer seeds germinated. There was also a reduction in shoot height with PLA. The biomass of A. rosea exposed to HDPE was significantly reduced compared to control samples. Furthermore, with HDPE present there was a decrease in soil pH. The size distribution of water-stable soil aggregates was altered when microplastics were present, suggesting potential alterations of soil stability. This study provides evidence that microplastics manufactured of HDPE and PLA, and synthetic fibers can affect the development of L. perenne, health of A. rosea and basic, but crucial soil properties, with potential further impacts on soil ecosystem functioning.

Journal Reference: Bas Boots, Connor William Russell, Dannielle Senga Green. Effects of Microplastics in Soil Ecosystems: Above and Below Ground. Environmental Science & Technology, 2019; DOI: 10.1021/acs.est.9b03304

Advanced breeding paves the way for disease-resistant beans

Summary: Researchers are involved in the development and implementation of a method to efficiently breed for disease-resistant beans in different regions of the world. Their work will help to improve the livelihood and food security of smallholders in developing countries. 

Angular leaf spot (ALS) is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) and causes serious yield losses worldwide. ALS resistance is reportedly pathotype-specific, but little is known about the efficacy of resistance loci against different pathotypes. Here, we report on ALS resistance evaluations of 316 bean lines under greenhouse and field conditions at multiple sites in Colombia and Uganda. Surprisingly, genome-wide association studies revealed only two of the five previously described resistance loci to be significantly associated with ALS resistance. Phg-2 on chromosome eight was crucial for ALS resistance in all trials, while the resistance locus Phg-4 on chromosome 4 was effective against one particular pathotype. Further dissection of Phg-2 uncovered an unprecedented diversity of functional haplotypes for a resistance locus in common bean. DNA sequence-based clustering identified eleven haplotype groups at Phg-2. One haplotype group conferred broad-spectrum ALS resistance, six showed pathotype-specific effects, and the remaining seven did not exhibit clear resistance patterns. Our research highlights the importance of ALS pathotype-specificity for durable resistance management strategies in common bean. Molecular markers co-segregating with resistance loci and haplotypes will increase breeding efficiency for ALS resistance and allow to react faster to future changes in pathogen pressure and composition.

Journal Reference: Michelle M. Nay, Clare M. Mukankusi, Bruno Studer, Bodo Raatz. Haplotypes at the Phg-2 Locus Are Determining Pathotype-Specificity of Angular Leaf Spot Resistance in Common Bean. Frontiers in Plant Science, 2019; 10 DOI: 10.3389/fpls.2019.01126

New way to test for drug resistant infections

Scientists have developed a method to test whether an infection is resistant to common antibiotics

Abstract: Antimicrobial resistance (AMR) has been identified as a major threat to public health worldwide. To ensure appropriate use of existing antibiotics, rapid and reliable tests of AMR are necessary. 

One of the most common and clinically important forms of bacterial resistance is to β-lactam antibiotics (e.g., penicillin). This resistance is often caused by β-lactamases, which hydrolyze β-lactam drugs, rendering them ineffective. Current methods for detecting these enzymes require either time-consuming growth assays or antibiotic mimics such as nitrocefin. Here, we report the development of a surface-bound, clinically relevant β-lactam drug that can be used to detect β-lactamases and that is compatible with a range of high-sensitivity, low-cost, and label-free analytical techniques currently being developed for point-of-care-diagnostics. Furthermore, we demonstrate the use of these functionalized surfaces to selectively detect β-lactamases in complex biological media, such as urine.

Journal Reference: Lisa M. Miller, Callum D. Silver, Reyme Herman, Anne-Kathrin Duhme-Klair, Gavin H. Thomas, Thomas F. Krauss, Steven D. Johnson. Surface-Bound Antibiotic for the Detection of β-Lactamases. ACS Applied Materials & Interfaces, 2019; DOI: 10.1021/acsami.9b05793

Nanowires replace Newton's famous glass prism

Summary: Scientists have designed an ultra-miniaturized device that could directly image single cells without the need for a microscope or make chemical fingerprint analysis possible from a smartphone. 

The device, made from a single nanowire 1000 times thinner than a human hair, is the smallest spectrometer ever designed. It could be used in potential applications such as assessing the freshness of foods, the quality of drugs, or even identifying counterfeit objects, all from a smartphone camera. Details are reported in the journal Science.

Spectrometers with ever-smaller footprints are sought after for a wide range of applications in which minimized size and weight are paramount, including emerging in situ characterization techniques. We report on an ultracompact microspectrometer design based on a single compositionally engineered nanowire. This platform is independent of the complex optical components or cavities that tend to constrain further miniaturization of current systems. We show that incident spectra can be computationally reconstructed from the different spectral response functions and measured photocurrents along the length of the nanowire. Our devices are capable of accurate, visible-range monochromatic and broadband light reconstruction, as well as spectral imaging from centimeter-scale focal planes down to lensless, single-cell–scale in situ mapping.

Journal Reference: Zongyin Yang, Tom Albrow-Owen, Hanxiao Cui, Jack Alexander-Webber, Fuxing Gu, Xiaomu Wang, Tien-Chun Wu, Minghua Zhuge, Calum Williams, Pan Wang, Anatoly V. Zayats, Weiwei Cai, Lun Dai, Stephan Hofmann, Mauro Overend, Limin Tong, Qing Yang, Zhipei Sun, Tawfique Hasan. Single-nanowire spectrometers. Science, 2019; 365 (6457): 1017 DOI: 10.1126/science.aax8814

Coffee may protect against gallstones

Summary: Drinking more coffee may help reduce the risk of developing gallstones, according to a new study. 

Journal Reference: A. T. Nordestgaard, S. Stender, B. G. Nordestgaard, A. Tybjærg‐Hansen. Coffee intake protects against symptomatic gallstone disease in the general population: a Mendelian randomization study. Journal of Internal Medicine, 2019; DOI: 10.1111/joim.12970

How plants decide between growth or defense

Summary: During their daily quest for survival, plants need to strike a careful balance between growth and defence. Both functions are vital for their successful reproduction, however, most plants are not able to do both at the same time.

The mechanisms behind this peculiar trade-off are little understood and it has often been hypothesised that restricted energy availability is the main limiting cause.

Grow or defend yourself -- a decision plants need to make on a daily basis, due to their inability to do both simultaneously. For a long time, it was thought that the reason for the growth-defence trade-off might be a question of energy resources. When a plant is defending itself against pathogens, energy could simply be limited for the plant to be growing at the same time, and vice versa. A recent paper published in Cell Reports shines a new light on the poorly understood mechanisms of the trade-off, clarifying that the actual underlying reasons is the incompatibility of the molecular pathways regulating plant growth and defence.

Journal Reference: Jakob Neuser, Caroline C. Metzen, Bernd H. Dreyer, Claudio Feulner, Joost T. van Dongen, Romy R. Schmidt, Jos H.M. Schippers. HBI1 Mediates the Trade-off between Growth and Immunity through Its Impact on Apoplastic ROS Homeostasis. Cell Reports, 2019; 28 (7): 1670 DOI: 10.1016/j.celrep.2019.07.029

New biosensor provides insight into the stress behavior of plants

Summary: Researchers have developed a method with which they can further investigate an important messenger substance in plants -- phosphatidic acid. Using a new biosensor, they are able to track the activity of phosphatidic acid spatially and temporally for the first time and thus, investigate plants that are exposed to stress such as salty soils. 

The newly developed biosensor is based on the principle of fluorescence resonance energy transfer (FRET). The sensor is a plasma membrane targeted fusion protein of a phosphatidic acid binding domain placed between two different fluorescent proteins that fluoresce blue and yellow when stimulated by light. Binding of phosphatidic acid to this sensor changes its conformation and this results in a change of the colour of the emitted light. Therefore, the new sensor is called "PAleon," which is derived from the abbreviation PA for phosphatidylic acid and chameleon. The scientists measure these signals using modern microscopy methods.

Journal Reference: Wenyu Li, Tengzhao Song, Lukas Wallrad, Jörg Kudla, Xuemin Wang, Wenhua Zhang. Tissue-specific accumulation of pH-sensing phosphatidic acid determines plant stress tolerance. Nature Plants, 2019; DOI: 10.1038/s41477-019-0497-6

Structure of protein nano turbine revealed

Summary: Scientists have determined the first structure of a cell's rotary engine using state-of-art microscopy.

Cells rely on protein complexes known as ATP synthases or ATPases for their energy needs -- adenosine triphosphate (ATP) molecules power most of the processes sustaining life. 

Structural biologist Professor Leonid Sazanov and his research group from the Institute of Science and Technology Austria (IST Austria) in Klosterneuburg, Austria have now determined the first atomic structure of the representative of the V/A-ATPase family, filling in the gap in the evolutionary tree of these essential molecular machines. These results obtained using the latest cryo-electron microscopy methods revealed a turbine or water mill similar structure of the enzyme and have now been published in the journal Science.

Journal Reference: Long Zhou, Leonid A. Sazanov. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science, 2019; 365 (6455): eaaw9144 DOI: 10.1126/science.aaw9144

Experiments illuminate key component of plants' immune systems

Understanding how plant resistance proteins trigger cell death could lead to strategies for engineering disease resistance in crops

Summary: Biologists have shed new light on a crucial aspect of the plant immune response. Their discovery, revealing how plant resistance proteins trigger localized cell death, could lead to new strategies for engineering disease resistance in next-generation crops.

Journal Reference: Li Wan, Kow Essuman, Ryan G. Anderson, Yo Sasaki, Freddy Monteiro, Eui-Hwan Chung, Erin Osborne Nishimura, Aaron Diantonio, Jeffrey Milbrandt, Jeffery L. Dangl, Marc T. Nishimura. TIR domains of plant immune receptors are NAD -cleaving enzymes that promote cell death. Science, 2019 DOI: 10.1126/science.aax1771

New insights into the origin of life

Did life begin from just the interactions between molecules of HCN and H2O in early, prebiotic Earth? The current, state-of-the-art, computational study indicates this is a likely possibility.

Summary: A famous experiment in 1953 showed that amino acids, the building blocks of proteins, could have formed spontaneously under the atmospheric conditions of early Earth. However, just because molecules could form doesn't mean that the process was likely. Now, researchers have demonstrated that energetically feasible interactions between just two small molecules -- hydrogen cyanide and water -- could give rise to most of the important precursors of RNA and proteins. To find out, the researchers used a recently developed tool called the ab initio nanoreactor, which simulates how mixtures of molecules can collide and react, forming new molecules.

Journal Reference: Tamal Das, Siddharth Ghule, Kumar Vanka. Insights Into the Origin of Life: Did It Begin from HCN and H2O? ACS Central Science, 2019; DOI: 10.1021/acscentsci.9b00520

Guacamole lovers, rejoice! The avocado genome has been sequenced

Summary: Scientists have sequenced the avocado genome, shedding light on the ancient origins of this buttery fruit and laying the groundwork for future improvements to farming. 

Journal Reference: Martha Rendón-Anaya, Enrique Ibarra-Laclette, Alfonso Méndez-Bravo, Tianying Lan, Chunfang Zheng, Lorenzo Carretero-Paulet, Claudia Anahí Perez-Torres, Alejandra Chacón-López, Gustavo Hernandez-Guzmán, Tien-Hao Chang, Kimberly M. Farr, W. Brad Barbazuk, Srikar Chamala, Marek Mutwil, Devendra Shivhare, David Alvarez-Ponce, Neena Mitter, Alice Hayward, Stephen Fletcher, Julio Rozas, Alejandro Sánchez Gracia, David Kuhn, Alejandro F. Barrientos-Priego, Jarkko Salojärvi, Pablo Librado, David Sankoff, Alfredo Herrera-Estrella, Victor A. Albert, and Luis Herrera-Estrella. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. PNAS, 2019 DOI: 10.1073/pnas.1822129116

How microorganisms protect themselves against free radicals

Summary: There are numerous different scenarios in which microorganisms are exposed to highly reactive molecules known as free radicals. These molecules are capable of damaging important cell components and may be generated during normal cell metabolism or in response to environmental factors. 

A team of researchers has discovered a previously unknown mechanism which enables microorganisms to protect themselves against free radicals. Their findings may help improve the efficacy of antimicrobial substances. 
Abstract: Both single and multicellular organisms depend on anti-stress mechanisms that enable them to deal with sudden changes in the environment, including exposure to heat and oxidants. Central to the stress response are dynamic changes in metabolism, such as the transition from the glycolysis to the pentose phosphate pathway—a conserved first-line response to oxidative insults. Here we report a second metabolic adaptation that protects microbial cells in stress situations. The role of the yeast polyamine transporter Tpo1p in maintaining oxidant resistance is unknown. However, a proteomic time-course experiment suggests a link to lysine metabolism. We reveal a connection between polyamine and lysine metabolism during stress situations, in the form of a promiscuous enzymatic reaction in which the first enzyme of the polyamine pathway, Spe1p, decarboxylates lysine and forms an alternative polyamine, cadaverine. The reaction proceeds in the presence of extracellular lysine, which is taken up by cells to reach concentrations up to one hundred times higher than those required for growth. Such extensive harvest is not observed for the other amino acids, is dependent on the polyamine pathway and triggers a reprogramming of redox metabolism. As a result, NADPH—which would otherwise be required for lysine biosynthesis—is channelled into glutathione metabolism, leading to a large increase in glutathione concentrations, lower levels of reactive oxygen species and increased oxidant tolerance. Our results show that nutrient uptake occurs not only to enable cell growth, but when the nutrient availability is favourable it also enables cells to reconfigure their metabolism to preventatively mount stress protection.

Journal Reference: Viridiana Olin-Sandoval, Jason Shu Lim Yu, Leonor Miller-Fleming, Mohammad Tauqeer Alam, Stephan Kamrad, Clara Correia-Melo, Robert Haas, Joanna Segal, David Alejandro Peña Navarro, Lucia Herrera-Dominguez, Oscar Méndez-Lucio, Jakob Vowinckel, Michael Mülleder, Markus Ralser. Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism. Nature, 2019; DOI: 10.1038/s41586-019-1442-6

The structural basis of N-acyl-α-amino-β-lactone formation catalyzed by a nonribosomal peptide synthetase.

β-Laktonové antibiotikum obafluorin. 
Abstract: Nonribosomal peptide synthetases produce diverse natural products using a multidomain architecture where the growing peptide, attached to an integrated carrier domain, is delivered to neighboring catalytic domains for bond formation and modification. 

Investigation of these systems can lead to the discovery of new structures, unusual biosynthetic transformations, and to the engineering of catalysts for generating new products. The antimicrobial β-lactone obafluorin is produced nonribosomally from dihydroxybenzoic acid and a β-hydroxy amino acid that cyclizes into the β-lactone during product release. Here we report the structure of the nonribosomal peptide synthetase ObiF1, highlighting the structure of the β-lactone-producing thioesterase domain and an interaction between the C-terminal MbtH-like domain with an upstream adenylation domain. Biochemical assays examine catalytic promiscuity, provide mechanistic insight, and demonstrate utility for generating obafluorin analogs. These results advance our understanding of the structural cycle of nonribosomal peptide synthetases and provide insights into the production of β-lactone natural products.

Obafluorin biosynthetic pathway. The NRPS catalytic cycle begins with (I) activation and loading of (2S,3R)-β-OH-p-NO2-homoPhe, generated by trans-aldol reaction of p-nitrophenylacetaldehyde (PNPAA) with a glycine enolate catalyzed by the L-Thr transaldolase ObiH, onto the ObiF1 PCP domain (T, green) by the ObiF1 adenylation domain (A, yellow). (II) Concurrently ObiF2 (AAr, yellow) activates 2,3-dihydroxybenzoic acid (2,3-DHB) and loads it onto ObiD (TAr, green). (III) Substrate-loaded ObiD then docks onto the ObiF C domain (C, blue), where the α-amino group of β-OH-p-NO2-homoPhe-T domain thioester is acylated by 2,3-DHB. (IV) Subsequent transthioesterification occurs between the substrate-loaded ObiF PCP domain and TE domain (TE, red) followed by TE domain catalyzed β-lactone formation and obafluorin release. The C-terminal MLP domain (purple) is highlighted to show interactions with the C and A domains of ObiF

Journal Reference: Dale F. Kreitler, Erin M. Gemmell, Jason E. Schaffer, Timothy A. Wencewicz, Andrew M. Gulick. The structural basis of N-acyl-α-amino-β-lactone formation catalyzed by a nonribosomal peptide synthetase. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-11383-7

Hidden chemistry in flowers shown to kill cancer cells

Summary: Researchers have shown that it's possible to produce a compound with anti-cancer properties directly from feverfew -- a common flowering garden plant (Řimbaba obecná). The compound the Birmingham team were investigating is called parthenolide and was identified by scientists as having anti-cancer properties several years ago. 

Although available commercially, it is extremely expensive with poor "drug-like" properties and has not progressed beyond basic research. 
The Birmingham team were able to show a method not only for producing the parthenolide directly from plants, but a way of modifying it to produce a number of compounds that killed cancer cells in in vitro experiments. The particular properties of these compounds make them much more promising as drugs that could be used in the clinic.

Upper: Structure of parthenolide (PTL, 1) and dimethyl amino-PTL (DMAPT) (2a) respectively; lower flowers of feverfew and a button-like (Tanacetum parthenium ‘Flore Pleno’) feverfew varietal. Feverfew = řimbaba obecná (Tanacetum parthenium) je středně vysoká, vytrvalá, aromatická rostlina s množstvím drobných květních úborů podobných kopretině. Na základě nových výzkumů byl rod (Pyrethrum) zrušen a jeho druhy, které se v české přírodě vyskytují, byly začleněny do rodu vratič (Tanacetum). Bylina řimbaba obecná tak dostává nové vědecké jméno Tanacetum parthenium. V české literatuře však bývá stále uváděna pod jménem Pyrethrum parthenium, nebo ještě se starším Chrysanthemum parthenium.

Worm pheromones protect major crops

Summary: Protecting crops from pests and pathogens without using toxic pesticides has been a longtime goal of farmers. Researchers have found that compounds from an unlikely source - microscopic soil roundworms - could achieve this aim. 

These compounds helped protect major crops from various pathogens, and thus have potential to save billions of dollars and increase agricultural sustainability around the world. 
Led by BTI Senior Research Associate Murli Manohar, a team around Professors Daniel Klessig and Frank Schroeder investigated the effects of a roundworm metabolite called ascr#18 on plant health. 
Ascr#18 is a member of the ascaroside family of pheromones, which are produced by many soil-dwelling species of roundworms for chemical communication. The researchers treated soybean (Glycine max), rice (Oryza sativa), wheat (Triticum aestivum) and maize (Zea mays) plants with small amounts of ascr#18, and then infected the plants with a virus, bacteria, fungus or oocmycete. 
When examined several days later, the ascr#18-treated plants were significantly more resistant to the pathogens compared with untreated plants. 
"Plant roots are constantly exposed to roundworms in the soil, so it makes sense that plants have evolved to sense the pest and prime their immune systems in anticipation of being attacked," says Schroeder.

Journal Reference: Daniel F. Klessig, Murli Manohar, Shine Baby, Aline Koch, Wiseborn B. Danquah, Emily Luna, Hee‐Jin Park, Judith M. Kolkman, B. Gillian Turgeon, Rebecca Nelson, Jan E. Leach, Valerie M. Williamson, Karl‐Heinz Kogel, Aardra Kachroo, Frank C. Schroeder. Nematode ascaroside enhances resistance in a broad spectrum of plant–pathogen systems. Journal of Phytopathology, 2019; 167 (5): 265 DOI: 10.1111/jph.12795

Biochemistry: Versatile recycling in the cell. New insights into ribosome recycling with enzyme ABCE1

Summary: Ribosomes need regenerating. This process is important for the quality of the proteins produced and thus for the whole cell homeostasis as well as for developmental and biological processes. 

Biochemists and biophysicists have now watched one of the most important enzymes for ribosome recycling at work -- ABCE1 -- and shown that it is unexpectedly versatile in terms of structure.

Journal Reference: Giorgos Gouridis, Bianca Hetzert, Kristin Kiosze-Becker, Marijn de Boer, Holger Heinemann, Elina Nürenberg-Goloub, Thorben Cordes, Robert Tampé. ABCE1 Controls Ribosome Recycling by an Asymmetric Dynamic Conformational Equilibrium. Cell Reports, 2019; 28 (3): 723 DOI: 10.1016/j.celrep.2019.06.052 PDF:

The emerging and uncultivated potential of CRISPR technology in plant science Review

Summary: CRISPR is often thought of as "molecular scissors" used for precision breeding to cut DNA so that a certain trait can be removed, replaced, or edited, but Yiping Qi, assistant professor in Plant Science & Landscape Architecture at the University of Maryland, is looking far beyond these traditional applications in his latest publication in Nature Plants. 

In this comprehensive review, Qi and coauthors in his lab explore the current state of CRISPR in crops, and how scientists can use CRISPR to enhance traditional breeding techniques in nontraditional ways, with the goal of ensuring global food and nutritional security and feeding a growing population in the face of climate change, diseases, and pests. The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.

Journal Reference: Yiping Qi et al. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019 DOI: 10.1038/s41477-019-0461-5

New study on the immune system of plants: It works differently than expected

Summary: What happens at the molecular level when plants defend against invading pathogens? Previously it was assumed that the processes were roughly the same in all plants. This is not true, as a team of biologists shows in a new study. 

The researchers investigated defense processes in the wild tobacco plant N. benthamiana and found that the processes work quite differently than previously thought.

Journal Reference: Johannes Gantner, Jana Ordon, Carola Kretschmer, Raphael Guerois, Johannes Stuttmann. An EDS1-SAG101 Complex is Essential for TNL-mediated Immunity in Nicotiana benthamiana. The Plant Cell, 2019; tpc.00099.2019 DOI: 10.1105/tpc.19.00099

Gene identified that will help develop plants to fight climate change

Finding will advance initiative to reduce atmospheric carbon through plants

Summary: Hidden underground networks of plant roots snake through the earth foraging for nutrients and water, similar to a worm searching for food. 

Yet, the genetic and molecular mechanisms that govern which parts of the soil roots explore remain largely unknown. Now, researchers have discovered a gene that determines whether roots grow deep or shallow in the soil. 

Journal Reference: Takehiko Ogura, Christian Goeschl, Daniele Filiault, Madalina Mirea, Radka Slovak, Bonnie Wolhrab, Santosh B. Satbhai, Wolfgang Busch. Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport. Cell, 2019; 178 (2): 400 DOI: 10.1016/j.cell.2019.06.021

Heat, salt, drought: This barley can withstand the challenges of climate change

Summary: Research for the benefit of food security: A new line of barley achieves good crop yields even under poor environmental conditions. It has been bred by a research team from Martin Luther University Halle-Wittenberg (MLU), 

which crossed a common variety with various types of wild barley. The researchers then planted the new lines of barley in five very different locations around the world, observed the growth of the plants and analysed their genetic make-up. As the team reports in "Scientific Reports," some of the plants were not only more resistant to heat and drought, but in many cases achieve higher yields than local varieties.

Conclusion: It is expected that the impact of climate change necessitates the adaptation of our established crop cultivation systems to harsher environmental conditions26,96. Stress avoidance is one promising approach to increase stress tolerance. We explored this relationship by studying the wild barley-derived model population HEB-YIELD in a field experiment, ranging from Dundee in Scotland to Adelaide in South Australia, where the effects of nitrogen deficiency, drought and salinity on plant development and yield-related traits were investigated. Our findings confirm the crucial relationship between flowering time, plant development and grain yield99. The exact timing of the switch from vegetative to reproductive growth under favorable conditions32, the length of the growing period and the duration of the sub-phases of plant development are crucial to secure yield under abiotic stress conditions. We suggest that adjusting plant development may be a promising breeding strategy to cope with abiotic stresses. To optimize breeding programs, it is thus advisable to first predict the environment-dependent impact of flowering time genes on yield formation and then to select locally advantageous alleles for sustainable crop improvement. Our HEB-YIELD data indicate that wild germplasm may serve as a resource to increase genetic diversity14,20,22 and to enable the above mentioned adaptation to abiotic stresses, through selection of early or late development alleles of known major flowering time genes, e.g. Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3. We showed that allelic variants of these flowering time genes strongly react to environmental cues. This information can be used to design novel breeding strategies such as precise backcrossing of suitable developmental genes into regionally adapted cultivars. Our data also provide evidence that wild barley germplasm may be useful to improve yield in low-yielding environments, for instance, in the Middle East, as well as in high-yielding environments, for instance, in Northern and Central Europe. This knowledge may be transferred to related crop species like wheat and rice to secure the rising global food demand for cereals.

Journal Reference: Mathias Wiegmann, Andreas Maurer, Anh Pham, Timothy J. March, Ayed Al-Abdallat, William T. B. Thomas, Hazel J. Bull, Mohammed Shahid, Jason Eglinton, Michael Baum, Andrew J. Flavell, Mark Tester, Klaus Pillen. Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues. Scientific Reports, 2019; 9 (1) DOI: 10.1038/s41598-019-42673-1

Gene-editing enzymes in action

Findings hold promise for future treatment of human diseases caused by DNA mutations

Summary: For the first time, scientists have captured high-resolution, three-dimensional images of an enzyme in the process of precisely cutting DNA strands.

The images -- captured using a technique called cryogenic electron microscopy, or cryo-EM -- reveal new information about how a gene-editing tool called CRISPR-Cas9 works, which may help researchers develop versions of it that operate more efficiently and precisely to alter targeted genes.

The findings - published today in Nature Structural and Molecular Biology -- hold promise for future treatment and prevention of a range of human diseases caused by DNA mutations, from cancer to cystic fibrosis and Huntington disease.

Journal Reference: Xing Zhu, Ryan Clarke, Anupama K. Puppala, Sagar Chittori, Alan Merk, Bradley J. Merrill, Miljan Simonović, Sriram Subramaniam. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nature Structural & Molecular Biology, 2019; DOI: 10.1038/s41594-019-0258-2

Researchers can finally modify plant mitochondrial DNA

Tool could ensure genetic diversity of crops

Summary: Researchers have edited plant mitochondrial DNA for the first time, which could lead to a more secure food supply. Nuclear DNA was first edited in the early 1970s, chloroplast DNA was first edited in 1988, and animal mitochondrial DNA was edited in 2008. 

However, no tool previously successfully edited plant mitochondrial DNA. Researchers used their technique to create four new lines of rice and three new lines of rapeseed (canola).

Journal References:
1. T. Kazama, M. Okuno, Y. Watari, S. Yanase, C. Koizuka, Y. Tsuruta, H. Sugaya, A. Toyoda, T. Itoh, N. Tsutsumi, K. Toriyama, N. Koizuka, S. Arimura. Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. Nature Plants, 2019 DOI: 10.1038/s41477-019-0459-z
2. S.-i. Arimura, J. Yamamoto, G. P. Aida, M. Nakazono, N. Tsutsumi. Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution. Proceedings of the National Academy of Sciences, 2004; 101 (20): 7805 DOI: 10.1073/pnas.0401077101

Scientists discover how plants breathe -- and how humans shaped their 'lungs'

Summary: Experts reveal how plants provide a steady flow of air to every cell. Study shows humans have bred wheat plants to have fewer pores on their leaves and use less water.

Findings pave the way to develop more drought-resistant crops. The new study, led by scientists at the University of Sheffield's Institute for Sustainable Food and published in Nature Communications, used genetic manipulation techniques to reveal that the more stomata a leaf has, the more airspace it forms. The channels act like bronchioles -- the tiny passages that carry air to the exchange surfaces of human and animal lungs.

Journal Reference: Marjorie R. Lundgren, Andrew Mathers, Alice L. Baillie, Jessica Dunn, Matthew J. Wilson, Lee Hunt, Radoslaw Pajor, Marc Fradera-Soler, Stephen Rolfe, Colin P. Osborne, Craig J. Sturrock, Julie E. Gray, Sacha J. Mooney, Andrew J. Fleming. Mesophyll porosity is modulated by the presence of functional stomata. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-10826-5

Could coffee be the secret to fighting obesity?

Summary: Scientists have discovered that drinking a cup of coffee can stimulate 'brown fat', the body's own fat-fighting defenses, which could be the key to tackling obesity and diabetes.

In conclusion, these results provide new complementary in vitro and in vivo evidence that caffeine (and a coffee beverage) can promote BAT function at doses compatible with human use. 

Similar approaches could be considered to screen other potential dietary compounds that could target UCP1 and promote BAT function. Future intervention studies can now be undertaken to assess whether caffeine-induced BAT activation in humans is dose-dependent, refine the minimal intake required for a BAT response, and explore whether comparable effects are seen in fully differentiated adipocytes and primary cells, as well as in diabetic and/or obese individuals. BAT = Brown adipose tissue; UCP1 = uncoupling protein 1

Journal Reference: Ksenija Velickovic, Declan Wayne, Hilda Anaid Lugo Leija, Ian Bloor, David E. Morris, James Law, Helen Budge, Harold Sacks, Michael E. Symonds, Virginie Sottile. Caffeine exposure induces browning features in adipose tissue in vitro and in vivo. Scientific Reports, 2019; 9 (1) DOI: 10.1038/s41598-019-45540-1

Engineering enzymes to turn plant waste into sustainable products

Summary: A new family of enzymes has been engineered to perform one of the most important steps in the conversion of plant waste into sustainable and high-value products such as nylon, plastics and chemicals.

Journal Reference: Melodie M. Machovina, Sam J. B. Mallinson, Brandon C. Knott, Alexander W. Meyers, Marc Garcia-Borràs, Lintao Bu, Japheth E. Gado, April Oliver, Graham P. Schmidt, Daniel J. Hinchen, Michael F. Crowley, Christopher W. Johnson, Ellen L. Neidle, Christina M. Payne, Kendall N. Houk, Gregg T. Beckham, John E. McGeehan, Jennifer L. DuBois. Enabling microbial syringol conversion through structure-guided protein engineering. Proceedings of the National Academy of Sciences, 2019; 201820001 DOI: 10.1073/pnas.1820001116

Honeybees infect wild bumblebees through shared flowers

Domestic beehives linked to spike in viral infections in nearby bumblebee populations

Summary: Viruses in managed honeybees are spilling over to wild bumblebee populations though the shared use of flowers, a first-of-its-kind study reveals. 

This research suggests commercial apiaries may need to be kept away from areas where there are vulnerable native pollinator species, like the endangered rusty patched bumblebee. Many species of wild bumblebees are in decline -- and new research shows that diseases spread by domestic honeybees may be a major culprit.

Journal Reference: Samantha A. Alger, P. Alexander Burnham, Humberto F. Boncristiani, Alison K. Brody. RNA virus spillover from managed honeybees (Apis mellifera) to wild bumblebees (Bombus spp.). PLOS ONE, 2019; 14 (6): e0217822 DOI: 10.1371/journal.pone.0217822

Plants' oil-production accelerator also activates the brakes

Scientists discover seemingly paradoxical mechanism for regulating oil synthesis

Summary: Scientists studying plant biochemistry recently made a surprising discovery: They found that a protein that turns on oil synthesis also activates a protein that puts the brakes on the same process. 

They describe how this seemingly paradoxical system keeps oil precursors perfectly balanced to meet plants' needs.

Journal Reference: Hui Liu, Zhiyang Zhai, Kate Kuczynski, Jantana Keereetaweep, Jorg Schwender, John Shanklin. WRINKLED1 regulates BIOTIN ATTACHMENT DOMAIN-CONTAINING proteins that inhibit fatty acid synthesis. Plant Physiology, 2019; pp.00587.2019 DOI: 10.1104/pp.19.00587

Light-powered nano-organisms consume carbon dioxide, create eco-friendly plastics and fuels (11.6.2019)

Summary: Researchers have developed nanobio-hybrid organisms capable of using airborne carbon dioxide and nitrogen to produce a variety of plastics and fuels, a promising first step toward low-cost carbon sequestration and eco-friendly manufacturing for chemicals. 

University of Colorado Boulder researchers have developed nanobio-hybrid organisms capable of using airborne carbon dioxide and nitrogen to produce a variety of plastics and fuels, a promising first step toward low-cost carbon sequestration and eco-friendly manufacturing for chemicals.

Journal Reference: Yuchen Ding, John R. Bertram, Carrie Eckert, Rajesh Reddy Bommareddy, Rajan Patel, Alex Conradie, Samantha Bryan, Prashant Nagpal. Nanorg microbial factories: Light-driven renewable biochemical synthesis using quantum dot-bacteria nano-biohybrids. Journal of the American Chemical Society, 2019; DOI: 10.1021/jacs.9b02549

How old are your organs? To scientists' surprise, organs are a mix of young and old cells (6.6.2019)

Scientists discover cellular structures with extreme longevity, leading to insights for age-associated diseases

Summary: Scientists once thought that neurons, or possibly heart cells, were the oldest cells in the body.

Now, researchers have discovered that the mouse brain, liver and pancreas contain populations of cells and proteins with extremely long lifespans -- some as old as neurons. Determining the age of cells and subcellular structures in adult organisms will provide new insights into cell maintenance and repair mechanisms and the impact of cumulative changes during adulthood on health and development of disease," adds Hetzer. "The ultimate goal is to utilize these mechanisms to prevent or delay age-related decline of organs with limited cell renewal."

Journal Reference: Rafael Arrojo e Drigo, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, Victoria Orphan, Claude Lechene, Mark H. Ellisman, Martin W. Hetzer. Age Mosaicism across Multiple Scales in Adult Tissues. Cell Metabolism, 2019; DOI: 10.1016/j.cmet.2019.05.010

Red and white meats are equally bad for cholesterol (4.6. 2019)

Summary: Contrary to popular belief, consuming red meat and white meat such as poultry, have equal effects on blood cholesterol levels, according to a study published today in the American Journal of Clinical Nutrition.

Journal Reference: Nathalie Bergeron, Sally Chiu, Paul T Williams, Sarah M King, Ronald M Krauss. Effects of red meat, white meat, and nonmeat protein sources on atherogenic lipoprotein measures in the context of low compared with high saturated fat intake: a randomized controlled trial. The American Journal of Clinical Nutrition, 2019; DOI: 10.1093/ajcn/nqz035

Genetic analysis of cannabis is here (29.5. 2019)

Summary: Research from Washington State University could provide government regulators with powerful new tools for addressing a bevy of commercial claims and other concerns as non-medical marijuana, hemp and CBD products become more commonplace. The new analysis of the genetic and chemical characteristics of cannabis is believed to be the first thorough examination of its kind.

Lange and his colleagues analyzed genetic sequences from nine commercial cannabis strains and found distinct gene networks orchestrating each strain's production of cannabinoid resins and terpenes, volatile compounds behind the plant's powerful aroma. Armed with this new tool, people can start to sort out a variety of issues that are already emerging as recreational cannabis is legal in 11 states, including the entire West Coast, and hemp is legal across the country. Lange's analytical method, for example, can be used to clearly delineate between psychoactive cannabis and hemp, which by law has to have less than 0.3 percent THC. It might help identify the skunky smell that elicits complaints from the neighbors of pot farms, opening a way to breed and grow something easier on the nose. It can test the health claims of cannabidiol, known by the shorthand CBD, or the alleged synergy, known as the "entourage effect," between cannabis compounds.

Journal Reference: Jordan J Zager, Iris Lange, Narayanan Srividya, Anthony Smith, Bernd Markus Lange. Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis. Plant Physiology, 2019; pp.01506.2018 DOI: 10.1104/pp.18.01506

Research team throws new light on photosynthetic supercomplex structure (27.5.2019)

Summary: A team of scientists from Arizona State University has taken a significant step closer to unlocking the secrets of photosynthesis, by determining the structure of a very large photosynthetic supercomplex.

Indeed it is this technique utilized by the experts in the School of Molecular Sciecnes and The College of Liberal Arts and Sciences at ASU that has enabled the elucidation of the structure of the PSI-IsiA complex. In the lab, this particular super-complex is produced by cyanobacteria under low iron environment or excessive light fluxes. However, in the "real world" iron exists at very low concentrations and high light can be the rule rather than the exception, so ultimately PSI-IsiA is a very common form of photosystem I, one of the two essential engines of photosynthesis. The complex is unique in size, the largest photosynthetic supercomplex with a known molecular structure, and in complexity with more than 700 different molecules (mostly light-harvesting molecules) making up the complete structure. There are 591 chlorophylls in the PSI-IsiA supercomplex, by far the largest number of bound pigments in any of the photosynthetic super-complexes with known structures. The current structure uncovers the most crucial details of this enormous machine. As the first example from the cyanobacterial branch of the membrane embedded antenna proteins, it lays a path for evaluating the light-harvesting and photoprotection mechanism (from excess or fluctuating light conditions) in cyanobacteria.

Journal Reference: Hila Toporik, Jin Li, Dewight Williams, Po-Lin Chiu, Yuval Mazor. The structure of the stress-induced photosystem I–IsiA antenna supercomplex. Nature Structural & Molecular Biology, 2019; DOI: 10.1038/s41594-019-0228-8

Plant stem cells require low oxygen levels (23.5.2019)

Summary: New research reveals that low oxygen is required for proper development of plants. Plants function as the green lungs of our planet. Rightfully so, due to the capacity of a large single tree releasing more than 120 kg of oxygen into the Earth's atmosphere every year through a series of sunlight-fuelled reactions in photosynthesis. 

However during flood events, plant tissues may experience severe oxygen shortage, a stressful situation that every year leads to substantial loss in yield for all major crops such as rice, wheat and barley. Complex multicellular organisms evolved on Earth in an oxygen-rich atmosphere1; their tissues, including stem-cell niches, require continuous oxygen provision for efficient energy metabolism2. Notably, the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation3. Here we demonstrate, using a combination of genetic reporters and in vivo oxygen measurements, that plant shoot meristems develop embedded in a low-oxygen niche, and that hypoxic conditions are required to regulate the production of new leaves. We show that hypoxia localized to the shoot meristem inhibits the proteolysis of an N-degron-pathway4,5 substrate known as LITTLE ZIPPER 2 (ZPR2)—which evolved to control the activity of the class-III homeodomain-leucine zipper transcription factors6,7,8—and thereby regulates the activity of shoot meristems. Our results reveal oxygen as a diffusible signal that is involved in the control of stem-cell activity in plants grown under aerobic conditions, which suggests that the spatially distinct distribution of oxygen affects plant development. In molecular terms, this signal is translated into transcriptional regulation by the N-degron pathway, thereby linking the control of metabolic activity to the regulation of development in plants.

Journal Reference: Daan A. Weits, Alicja B. Kunkowska, Nicholas C. W. Kamps, Katharina M. S. Portz, Niko K. Packbier, Zoe Nemec Venza, Christophe Gaillochet, Jan U. Lohmann, Ole Pedersen, Joost T. van Dongen, Francesco Licausi. An apical hypoxic niche sets the pace of shoot meristem activity. Nature, 2019; DOI: 10.1038/s41586-019-1203-6

Dietary cholesterol or egg consumption do not increase the risk of stroke, Finnish study finds (20.5. 2019)

Summary: A new study Finland shows that a moderately high intake of dietary cholesterol or consumption of up to one egg per day is not associated with an elevated risk of stroke. Furthermore, no association was found in carriers of the APOE4 phenotype, 

which affects cholesterol metabolism and is remarkably common among the Finnish population.

Journal Reference: Anna M Abdollahi, Heli E K Virtanen, Sari Voutilainen, Sudhir Kurl, Tomi-Pekka Tuomainen, Jukka T Salonen, Jyrki K Virtanen. Egg consumption, cholesterol intake, and risk of incident stroke in men: the Kuopio Ischaemic Heart Disease Risk Factor Study. The American Journal of Clinical Nutrition, 2019; DOI: 10.1093/ajcn/nqz066

Natural compound found in broccoli reawakens the function of potent tumor suppressor Finding offers potential novel approach to cancer treatment and prevention (16.5.2019)

Summary: Long associated with decreased risk of cancer, broccoli and other cruciferous vegetables -- the family of plants that also includes cauliflower, cabbage, collard greens, Brussels sprouts and kale -- contain a molecule that inactivates a gene known to play a role in a variety of common human cancers.

A new study demonstrates that targeting the gene, known as WWP1, with the ingredient found in broccoli suppressed tumor growth in cancer-prone lab animals.

Journal Reference: Yu-Ru Lee, Ming Chen, Jonathan D. Lee, Jinfang Zhang, Shu-Yu Lin, Tian-Min Fu, Hao Chen, Tomoki Ishikawa, Shang-Yin Chiang, Jesse Katon, Yang Zhang, Yulia V. Shulga, Assaf C. Bester, Jacqueline Fung, Emanuele Monteleone, Lixin Wan, Chen Shen, Chih-Hung Hsu, Antonella Papa, John G. Clohessy, Julie Teruya-Feldstein, Suresh Jain, Hao Wu, Lydia Matesic, Ruey-Hwa Chen, Wenyi Wei, Pier Paolo Pandolfi. Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway. Science, 2019; 364 (6441): eaau0159 DOI: 10.1126/science.aau0159

Rice blast fungus study sheds new light on virulence mechanisms of plant pathogenic fungi (14.5.2019)

Summary: Rice blast fungus (Magnaporthe oryzae) is a global food security threat due to its destruction of cultivated rice, the most widely consumed staple food in the world. Disease containment efforts using traditional breeding or chemical approaches have been unsuccessful as the fungus can rapidly adapt and mutate to develop resistance. 

Because of this, it is necessary to understand fungal infection-related development to formulate new, effective methods of blast control. On a large scale, these findings shed a new light on the eukaryotic cell biology and virulence mechanisms of plant pathogenic fungi. On a smaller scale, these findings could reveal novel approaches or targets for anti-blast fungus management.

Journal Reference: Lianwei Li, Shengpei Zhang, Xinyu Liu, Rui Yu, Xinrui Li, Muxing Liu, Haifeng Zhang, Xiaobo Zheng, Ping Wang, Zhengguang Zhang. Magnaporthe oryzae Abp1, a MoArk1 Kinase-Interacting Actin Binding Protein, Links Actin Cytoskeleton Regulation to Growth, Endocytosis, and Pathogenesis. Molecular Plant-Microbe Interactions, 2019; 32 (4): 437 DOI: 10.1094/MPMI-10-18-0281-R

How potatoes could thrive in a warmer world. Researchers succeed in growing potatoes even at high temperatures (14.5.2019)

Summary: Biochemists at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) have now discovered the reason why. If the temperature rises, a so-called small RNA blocks the formation of tubers. The scientists have now successfully switched off this small RNA and have produced potato plants that are more resistant to high temperatures,

which is an important contribution to securing crop yields in the future in view of climate change. They have now presented their results in the journal Current Biology published by Cell Press.

Journal Reference: Günter G. Lehretz, Sophia Sonnewald, Csaba Hornyik, José M. Corral, Uwe Sonnewald. Post-transcriptional Regulation of FLOWERING LOCUS T Modulates Heat-Dependent Source-Sink Development in Potato. Current Biology, 2019; DOI: 10.1016/j.cub.2019.04.027

Tomato pan-genome makes bringing flavor back easier Nearly 5,000 new tomato genes mapped (13.5.2019)

Summary: Do you find that most store-bought tomatoes don't have much flavor? Scientists may have spotlighted the solution by developing the tomato pan-genome, mapping almost 5,000 previously undocumented genes, including genes for flavor. 

Journal Reference: Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Jose Blanca, Joaquin Canizares, Yimin Xu, Esther van der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni, Zhangjun Fei. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 2019; DOI: 10.1038/s41588-019-0410-2

Researchers crack the peanut genome. New genome map sheds light on ancestry, diversity of today's peanuts. (2.5.2019)

Summary: Working to understand the genetics of peanut disease resistance and yield, researchers led by scientists at the University of Georgia have uncovered the peanut's unlikely and complicated evolution. The researchers used new advances in DNA-sequencing technologies to produce a complete genome sequence of unprecedented quality.

The sequence consists of more than 2.5 billion base pairs of DNA arranged in 20 pairs of chromosomes, 10 pairs from each of the ancestral species. The information in the sequence sheds light on parts of the plant's genetic code that control traits like seed size and disease resistance, which are important to plant breeders. But the sequence also revealed more about the origin of peanut during the dawn of agriculture in South America and on the genetic mechanisms that have generated diversity and allowed adaptation to environments around the globe.

Journal Reference: David J. Bertioli, Jerry Jenkins, Josh Clevenger, Olga Dudchenko, Dongying Gao, Guillermo Seijo, Soraya C. M. Leal-Bertioli, Longhui Ren, Andrew D. Farmer, Manish K. Pandey, Sergio S. Samoluk, Brian Abernathy, Gaurav Agarwal, Carolina Ballén-Taborda, Connor Cameron, Jacqueline Campbell, Carolina Chavarro, Annapurna Chitikineni, Ye Chu, Sudhansu Dash, Moaine El Baidouri, Baozhu Guo, Wei Huang, Kyung Do Kim, Walid Korani, Sophie Lanciano, Christopher G. Lui, Marie Mirouze, Márcio C. Moretzsohn, Melanie Pham, Jin Hee Shin, Kenta Shirasawa, Senjuti Sinharoy, Avinash Sreedasyam, Nathan T. Weeks, Xinyou Zhang, Zheng Zheng, Ziqi Sun, Lutz Froenicke, Erez L. Aiden, Richard Michelmore, Rajeev K. Varshney, C. Corley Holbrook, Ethalinda K. S. Cannon, Brian E. Scheffler, Jane Grimwood, Peggy Ozias-Akins, Steven B. Cannon, Scott A. Jackson, Jeremy Schmutz. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics, 2019; DOI: 10.1038/s41588-019-0405-z

Discovery of RNA transfer through royal jelly could aid development of honey bee vaccines (2.5.2019)

Summary: Researchers have discovered that honey bees are able to share immunity with other bees and to their offspring in a hive by transmitting RNA 'vaccines' through royal jelly and worker jelly. The jelly is the bee equivalent of mother's milk: a secretion used to provide nutrition to worker and queen bee larvae.

The findings suggest new ways to protect bees against viruses and the deadly Varroa mite that have been responsible for the recent dramatic decline in honey bee populations. Since around one third of the human diet globally is dependent on honey bee pollination, we need solutions urgently to help maintain flourishing bee colonies, for our food security and sustainability.

Journal Reference: Eyal Maori, Yael Garbian, Vered Kunik, Rita Mozes-Koch, Osnat Malka, Haim Kalev, Niv Sabath, Ilan Sela, Sharoni Shafir. A Transmissible RNA Pathway in Honey Bees. Cell Reports, 2019; DOI: 10.1016/j.celrep.2019.04.073

Plant cells eat their own ... membranes and oil droplets. Autofágie jako způsob přežití rostlin bez sluneční fotosyntézy!! (29.4.2019)

Summary: Biochemists have discovered two ways that autophagy, or self-eating, controls the levels of oils in plant cells. The study describes how this cannibalistic-sounding process actually helps plants survive, and suggests a way to get bioenergy crops to accumulate more oil.

These images, taken using a confocal microscope at Brookhaven Lab's Center for Functional Nanomaterials, show lipid droplets (green) enclosed within plant cell vacuoles (red-labeled membranes). The plants had been in the dark and were in the process of "eating" their own lipid droplets to provide the cells with energy in the absence of sunlight/photosynthesis.

Journal Reference: Jilian Fan, Linhui Yu, Changcheng Xu. Dual Role for Autophagy in Lipid Metabolism in Arabidopsis. The Plant Cell, 2019 DOI: 10.1105/tpc.19.00170

Bringing information into the cell (25.4.2019)

Summary: Researchers have elucidated an important part of a signal pathway that transmits information through the cell membrane into the interior of a cell. This signal pathway is of great significance for all mammals, since it is involved in various important vital processes such as the regulation of the heartbeat.

The researchers achieved their results using cryo-electron microscopy (cryo-EM). This form of transmission electron microscopy operates at temperatures below -150 degrees Celsius. The sample to be examined is snap frozen in liquid ethane, preserving its natural structure. This method, for which the Nobel Prize for Chemistry was awarded in 2017, is increasingly used in the investigation of biological structures. "It is exciting to get a deep insight into the structure of adenylate cyclase," says Chao Qi, a doctoral candidate in Korkhov's lab and first author of the study. "The structure of this protein has been elusive for decades since its discovery, and I'm glad that I was able to elucidate this structure with cryo-EM in the course of my doctoral research." The resolution achieved by the PSI researchers in their investigations was 3.4 angstroms. An angstrom is one ten-millionth of a millimetre. Isolated atoms have a radius of 0.3 to 3 angstroms.

Journal Reference: Chao Qi, Simona Sorrentino, Ohad Medalia, Volodymyr M. Korkhov. The structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein. Science, 2019 DOI: 10.1126/science.aav0778

Left or right handed biomolecules (25.4.2019)

Summary: Many biomolecules come in two versions that are each other's mirror image, like a left and a right hand. Cells generally use the left-hand version of amino acids to produce proteins, and uptake mechanisms were thought to share this preference.

Scientists have now shown that a prokaryotic transport protein can transport both versions of the amino acid aspartate with equal efficiency.

This illustration shows L- and D-aspartate on the binding site of the transport protein.

Journal Reference: Valentina Arkhipova, Gianluca Trinco, Thijs W Ettema, Sonja Jensen, Dirk J Slotboom, Albert Guskov. Binding and transport of D-aspartate by the glutamate transporter homolog GltTk. eLife, 2019 DOI: 10.7554/eLife.45286.001

How plants defend themselves. Plant immune system detects bacteria through small fatty acid molecules (11.4.2019)

Summary: Like humans and animals, plants defend themselves against pathogens with the help of their immune system. But how do they activate their cellular defenses? Researchers have now discovered that receptors in plant cells identify bacteria through simple molecular building blocks.

Fitness program for plants: In the future, these results could help in breeding or genetically engineering plants with an improved immune response. It is also conceivable that plants treated with 3-hydroxy fatty acids would have increased resistance to pathogens.

Journal Reference: Alexander Kutschera, Corinna Dawid, Nicolas Gisch, Christian Schmid, Lars Raasch, Tim Gerster, Milena Schäffer, Elwira Smakowska-Luzan, Youssef Belkhadir, A. Corina Vlot, Courtney E. Chandler, Romain Schellenberger, Dominik Schwudke, Robert K. Ernst, Stéphan Dorey, Ralph Hückelhoven, Thomas Hofmann, Stefanie Ranf. Bacterial medium chain 3-hydroxy fatty acid metabolites trigger immunity in Arabidopsis plants. Science, 2019 DOI: 10.1126/science.aau1279