The ribosome is a molecular factory that translates the genetic information in RNA into a string of amino acids that becomes a protein. Inside the ribosome, the genetic code of the RNA is read three letters at a time and compared with the corresponding code on a transfer molecule. When a match occurs between the codes, the amino acid carried by the transfer molecule is added to the growing protein chain.
Ever since their discovery as key regulators of the jasmonate (JA) signaling pathway (Chini et al., 2007; Thines et al., 2007; Yan et al., 2007), repressor proteins of the JASMONATE ZIM-domain (JAZ) family have been rising stars in research on hormonal regulation of plant growth and defense. In plant cells, JAZ repressor proteins interact with an E3 ubiquitin ligase complex (SCFCOI1) that together function as a JA receptor. In resting cells, JAZs block the activity of transcriptional regulators of JA responses by physically binding to them. Upon perception of bioactive JAs, JAZ proteins are rapidly degraded via the ubiquitin/26S proteasome-dependent proteolytic pathway. This releases the JAZ-bound transcription factors, resulting in the activation of downstream JA responses (Fig. 1a). JAs play a dominant role in regulating defense responses against herbivorous insects and necrotrophic pathogens, and in adaptive responses to beneficial soilborne microbes (Wasternack & Hause, 2013; Pieterse et al., 2014). In addition, JAs have a signal function in a myriad other processes, including abiotic stress reactions and plant growth responses to environmental cues (Wasternack & Hause, 2013). The JA pathway functions in the context of a complex network of hormone-regulated signaling pathways that, depending on the environmental or developmental condition, can act antagonistically or synergistically on each other to finely balance resource allocation between growth and defense and minimize fitness tradeoffs (Pieterse et al., 2012; Vos et al., 2013). In the process of balancing plant growth and defense, gibberellins (GAs) have emerged as dominant antagonists of the JA signaling output (Hou et al., 2013).
Interesting new chemical genetics study identifies a compound that alleviates some of the low-Pi responses in plants. Treated plants grow better on low P, "this reveals that the developmental restrictions induced by Pi starvation are not a consequence of metabolic limitation, but also result from genetic regulation." (OPEN in Plant Phys)
To test the efficacy of CRISPR/Cas9 in tomato, we chose to target a gene that, when function was disrupted, would result in a distinctive, immediately recognizable phenotype early in the plant tissue culture phase of Agrobacterium-mediated transformation. A CRISPR/Cas9 construct was designed to target neighboring sequences in the second exon of the tomato homolog of Arabidopsis ARGONAUTE7 (SlAGO7), because loss-of-function mutations are recessive and result in plants whose typical compound flat leaves become needle-like, or “wiry” (Fig. 1) (Lesley, 1928; Yifhar et al., 2012). SlAGO7 is required for the biogenesis of a class of small RNAs known as trans-acting short interfering RNAs (ta-siRNAs), which regulate organ polarity through post-transcriptional silencing of AUXIN RESPONSE FACTOR (ARF) genes (Husbands et al., 2009). Strong alleles of slago7 thus produce lower levels of ta-siRNAs and reduced ARF mRNA degradation, resulting in the first leaves of mutant plants having leaflets without petioles, and later formed leaves lacking laminae (Fig. 1C). These distinctive phenotypes allowed us to immediately identify first generation transformed (T0) plants in which both alleles of SlAGO7 might be mutated.
While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.
Ralf Weßling, Petra Epple, Stefan Altmann,Yijian He, Li Yang, Stefan R. Henz, Nathan McDonald, Kristin Wiley, Kai Christian Bader, Christine Glaßer, M. Shahid Mukhtar, Sabine Haigis, Lila Ghamsari, Amber E. Stephens, Joseph R. Ecker, Marc Vidal, Jonathan D.G. Jones,Klaus F.X. Mayer, Emiel Ver Loren van Themaat, Detlef Weigel, Paul Schulze-Lefert, Jeffery L. Dangl, Ralph Panstruga, and Pascal Braun
"Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals."
A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional–structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.
In this first of three lessons spanning the topic of Plant Nutrition, we examine primarily the energetics and mechanisms of nutrient uptake and transport. These processes are particularly well illustrated by an examination of the essential nutrient potassium (K), and the closely related element sodium (Na). We also examine the challenges associated with providing plants with sufficient K to support vigorous growth, and the detrimental effects of sodium accumulation in soils. Finally, we examine efforts to improve the salinity tolerance of crop plants. (Co-authored with Michael Blatt).
"One of the most remarkable features of modern times is the combination of large numbers of individuals representing the whole intelligence of nations, for the express purpose of advancing science by their united efforts. The influence of (scientific truths) upon mental culture is most beneficial, and the new views acquired by the knowledge of them enable the mind to recognise in the phenomena of nature proofs of an infinite wisdom, the unfathomable profundity of which language has no expression."
Mary Williams's insight:
I love the last phrase - "the unfathomable profundity of which language has no expression". I think that captures the essence of being a scientist.
Researchers are trying to mimic the growing conditions expected to arise decades in the future as the air fills with heat-trapping gases and other pollutants from human activity, with some worrisome results.
Neurospora crassa has a long history as an excellent model for genetic, cellular, and biochemical research. Although this fungus is known as a saprotroph, it normally appears on burned vegetations or trees after forest fires. However, due to a lack of experimental evidence, the nature of its association with living plants remains enigmatic. Here we report that Scots pine (Pinus sylvestris) is a host plant for N. crassa. The endophytic lifestyle of N. crassa was found in its interaction with Scots pine. Moreover, the fungus can switch to a pathogenic state when its balanced interaction with the host is disrupted. Our data reveal previously unknown lifestyles of N. crassa, which are likely controlled by both environmental and host factors. Switching among the endophytic, pathogenic, and saprotrophic lifestyles confers upon fungi phenotypic plasticity in adapting to changing environments and drives the evolution of fungi and associated plants.
Vitamin A deficiency is a deadly threat to kids and pregnant mothers in the Third World. In the Philippines, the best nutrient sources are rarely part of the daily diet, so researchers have tried adding vitamin A to rice, a staple food. Science correspondent Miles O'Brien investigates the debate that’s grown up over the development of golden rice, a genetically modified crop. Continue reading →
•Autophagy can suppress, initiate, or execute cell death depending on the biological context.
•Autophagy is an initiator of localized, hypersensitive response-associated cell death upon pathogen infection.
•Autophagy executes ‘formative’ vacuolar cell death and prevents ‘destructive’ necrosis in terminally differentiated cells.
•Homeostatic and anti-aging functions of autophagy complicate the dissection of its distinct roles in cell death.
Autophagy plays multiple, often antagonistic roles in plants. In particular, cytoprotective functions of autophagy are well balanced by cell death functions to compensate for the absence of apoptosis culminating in phagocytic clearance of dead cells. If autophagy is indeed required for plant programmed cell death (PCD), then what place does it occupy in the PCD pathways? Recent studies have examined the effects of impaired autophagy on pathogen-induced hypersensitive response (HR) and developmental PCD. While HR death was efficiently suppressed, inhibition of autophagy induced a switch from vacuolar PCD essential for development to necrosis. We therefore propose a dual role for autophagy in plant PCD: as an effector of HR PCD lying upstream of the ‘point-of-no-return’, and also as a downstream mechanism for clearance of terminally differentiated cells during developmental PCD.
"In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications."
Mary Williams's insight:
Free from Cold Spring Harbor Perspectives in Biology - good for your teaching!
"As global population grows, are we ever going to run out of food? There are lots of people who say we need to work very hard to make farming more efficient to feed the word. Then there are others who say, no, the real problem is more equitably dividing the food up, and efficient farming techniques actually make the inequality worse. Finally, there are people who say that growing more, and sharing it better, doesn’t matter as long as keep making babies. Here we sort through the sweeping claims and look beyond the rhetoric to understand how to make food systems green and fair."
Mary Williams's insight:
I like his articles because they are clear, well-researched and accessible. Good resources for students!
Science, "The coffee genome provides insight into the convergent evolution of caffeine biosynthesis" "With more than 2.25 billion cups consumed every day, coffee is one of the most important crops on Earth, cultivated across more than 11 million hectares"
And one of the most important contributors to the efforts of scientists, too!