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Annual Review of Plant Biology

Natasha V Raikhel
I was a budding pianist immersed in music in Leningrad, in the Soviet Union (now Saint Petersburg, Russia), when I started over, giving up sheet music for the study of ciliates. In a second starting-over story, I emigrated to the United States, where I switched to studying carbohydrate-binding plant lectin proteins, dissecting plant vesicular trafficking, and isolating novel glycosyltransferases responsible for making cell wall polysaccharides. I track my journey as a plant biologist from student to principal investigator to founding director of the Center for Plant Cell Biology and then director of the Institute for Integrative Genome Biology at the University of California, Riverside...
November 16, 2016: Annual Review of Plant Biology
Amancio de Souza, Jin-Zheng Wang, Katayoon Dehesh
Interorganellar cooperation maintained via exquisitely controlled retrograde-signaling pathways is an evolutionary necessity for maintenance of cellular homoeostasis. This signaling feature has therefore attracted much research attention aimed at improving understanding of the nature of these communication signals, how the signals are sensed, and ultimately the mechanism by which they integrate targeted processes that collectively culminate in organellar cooperativity. The answers to these questions will provide insight into how retrograde-signal-mediated regulatory mechanisms are recruited and which biological processes are targeted, and will advance our understanding of how organisms balance metabolic investments in growth against adaptation to environmental stress...
November 2, 2016: Annual Review of Plant Biology
Satoko Yoshida, Songkui Cui, Yasunori Ichihashi, Ken Shirasu
Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae...
April 29, 2016: Annual Review of Plant Biology
Allison Gaudinier, Siobhan M Brady
In plants, systems biology approaches have led to the generation of a variety of large data sets. Many of these data are created to elucidate gene expression profiles and their corresponding transcriptional regulatory mechanisms across a range of tissue types, organs, and environmental conditions. In an effort to map the complexity of this transcriptional regulatory control, several types of experimental assays have been used to map transcriptional regulatory networks. In this review, we discuss how these methods can be best used to identify novel biological mechanisms by focusing on the appropriate biological context...
April 29, 2016: Annual Review of Plant Biology
Stephan Clemens, Jian Feng Ma
Arsenic, cadmium, lead, and mercury are toxic elements that are almost ubiquitously present at low levels in the environment because of anthropogenic influences. Dietary intake of plant-derived food represents a major fraction of potentially health-threatening human exposure, especially to arsenic and cadmium. In the interest of better food safety, it is important to reduce toxic element accumulation in crops. A molecular understanding of the pathways responsible for this accumulation can enable the development of crop varieties with strongly reduced concentrations of toxic elements in their edible parts...
April 29, 2016: Annual Review of Plant Biology
Julio Paez Valencia, Kaija Goodman, Marisa S Otegui
Endocytosis and endosomal trafficking are essential processes in cells that control the dynamics and turnover of plasma membrane proteins, such as receptors, transporters, and cell wall biosynthetic enzymes. Plasma membrane proteins (cargo) are internalized by endocytosis through clathrin-dependent or clathrin-independent mechanism and delivered to early endosomes. From the endosomes, cargo proteins are recycled back to the plasma membrane via different pathways, which rely on small GTPases and the retromer complex...
April 29, 2016: Annual Review of Plant Biology
Bob B Buchanan
After a brief discussion of my graduate work at Duke University, I describe a series of investigations on redox proteins at the University of California, Berkeley. Starting with ferredoxin from fermentative bacteria, the Berkeley research fostered experiments that uncovered a pathway for fixing CO2 in bacterial photosynthesis. The carbon work, in turn, opened new vistas, including the discovery that thioredoxin functions universally in regulating the Calvin-Benson cycle in oxygenic photosynthesis. These experiments, which took place over a 50-year period, led to the formulation of a set of biological principles and set the stage for research demonstrating a role for redox in the regulation of previously unrecognized processes extending far beyond photosynthesis...
April 29, 2016: Annual Review of Plant Biology
Won-Gyu Choi, Richard Hilleary, Sarah J Swanson, Su-Hwa Kim, Simon Gilroy
Plants integrate activities throughout their bodies using long-range signaling systems in which stimuli sensed by just a few cells are translated into mobile signals that can influence the activities in distant tissues. Such signaling can travel at speeds well in excess of millimeters per second and can trigger responses as diverse as changes in transcription and translation levels, posttranslational regulation, alterations in metabolite levels, and even wholesale reprogramming of development. In addition to the use of mobile small molecules and hormones, electrical signals have long been known to propagate throughout the plant...
April 29, 2016: Annual Review of Plant Biology
Wataru Yamori, Toshiharu Shikanai
The light reactions in photosynthesis drive both linear and cyclic electron transport around photosystem I (PSI). Linear electron transport generates both ATP and NADPH, whereas PSI cyclic electron transport produces ATP without producing NADPH. PSI cyclic electron transport is thought to be essential for balancing the ATP/NADPH production ratio and for protecting both photosystems from damage caused by stromal overreduction. Two distinct pathways of cyclic electron transport have been proposed in angiosperms: a major pathway that depends on the PROTON GRADIENT REGULATION 5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE 1 (PGRL1) proteins, which are the target site of antimycin A, and a minor pathway mediated by the chloroplast NADH dehydrogenase-like (NDH) complex...
April 29, 2016: Annual Review of Plant Biology
Markus Pauly, Kenneth Keegstra
Xyloglucan (XyG) is a matrix polysaccharide that is present in the cell walls of all land plants. It consists of a β-1,4-linked glucan backbone that is further substituted with xylosyl residues. These xylosyl residues can be further substituted with other glycosyl and nonglycosyl substituents that vary depending on the plant family and specific tissue. Advances in plant mutant isolation and characterization, functional genomics, and DNA sequencing have led to the identification of nearly all transferases and synthases necessary to synthesize XyG...
April 29, 2016: Annual Review of Plant Biology
Rubén Rellán-Álvarez, Guillaume Lobet, José R Dinneny
The plant root system traverses one of the most complex environments on earth. Understanding how roots support plant life on land requires knowing how soil properties affect the availability of nutrients and water and how roots manipulate the soil environment to optimize acquisition of these resources. Imaging of roots in soil allows the integrated analysis and modeling of environmental interactions occurring at micro- to macroscales. Advances in phenotyping of root systems is driving innovation in cross-platform-compatible methods for data analysis...
April 29, 2016: Annual Review of Plant Biology
Vidadi Yusibov, Natasha Kushnir, Stephen J Streatfield
Monoclonal antibodies (mAbs) have a wide range of modern applications, including research, diagnostic, therapeutic, and industrial uses. Market demand for mAbs is high and continues to grow. Although mammalian systems, which currently dominate the biomanufacturing industry, produce effective and safe recombinant mAbs, they have a limited manufacturing capacity and high costs. Bacteria, yeast, and insect cell systems are highly scalable and cost effective but vary in their ability to produce appropriate posttranslationally modified mAbs...
April 29, 2016: Annual Review of Plant Biology
Dolf Weijers, Doris Wagner
Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development...
April 29, 2016: Annual Review of Plant Biology
Mieke de Wit, Vinicius Costa Galvão, Christian Fankhauser
Light is crucial for plant life, and perception of the light environment dictates plant growth, morphology, and developmental changes. Such adjustments in growth and development in response to light conditions are often established through changes in hormone levels and signaling. This review discusses examples of light-regulated processes throughout a plant's life cycle for which it is known how light signals lead to hormonal regulation. Light acts as an important developmental switch in germination, photomorphogenesis, and transition to flowering, and light cues are essential to ensure light capture through architectural changes during phototropism and the shade avoidance response...
April 29, 2016: Annual Review of Plant Biology
Jens Tilsner, William Nicolas, Abel Rosado, Emmanuelle M Bayer
Multicellularity differs in plants and animals in that the cytoplasm, plasma membrane, and endomembrane of plants are connected between cells through plasmodesmal pores. Plasmodesmata (PDs) are essential for plant life and serve as conduits for the transport of proteins, small RNAs, hormones, and metabolites during developmental and defense signaling. They are also the only pathways available for viruses to spread within plant hosts. The membrane organization of PDs is unique, characterized by the close apposition of the endoplasmic reticulum and the plasma membrane and spoke-like filamentous structures linking the two membranes, which define PDs as membrane contact sites (MCSs)...
April 29, 2016: Annual Review of Plant Biology
Thomas Dobrenel, Camila Caldana, Johannes Hanson, Christophe Robaglia, Michel Vincentz, Bruce Veit, Christian Meyer
All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy...
April 29, 2016: Annual Review of Plant Biology
Lee E Vandivier, Stephen J Anderson, Shawn W Foley, Brian D Gregory
RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts...
April 29, 2016: Annual Review of Plant Biology
Berkley J Walker, Andy VanLoocke, Carl J Bernacchi, Donald R Ort
Photorespiration is essential for C3 plants but operates at the massive expense of fixed carbon dioxide and energy. Photorespiration is initiated when the initial enzyme of photosynthesis, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), reacts with oxygen instead of carbon dioxide and produces a toxic compound that is then recycled by photorespiration. Photorespiration can be modeled at the canopy and regional scales to determine its cost under current and future atmospheres. A regional-scale model reveals that photorespiration currently decreases US soybean and wheat yields by 36% and 20%, respectively, and a 5% decrease in the losses due to photorespiration would be worth approximately $500 million annually in the United States...
April 29, 2016: Annual Review of Plant Biology
Eric A Fich, Nicholas A Segerson, Jocelyn K C Rose
Cutin, a polyester composed mostly of oxygenated fatty acids, serves as the framework of the plant cuticle. The same types of cutin monomers occur across most plant lineages, although some evolutionary trends are evident. Additionally, cutins from some species have monomer profiles that are characteristic of the related polymer suberin. Compositional differences likely have profound structural consequences, but little is known about cutin's molecular organization and architectural heterogeneity. Its biological importance is suggested by the wide variety of associated mutants and gene-silencing lines that show a disruption of cuticular integrity, giving rise to numerous physiological and developmental abnormalities...
April 29, 2016: Annual Review of Plant Biology
Changcheng Xu, John Shanklin
Oils in the form of triacylglycerols are the most abundant energy-dense storage compounds in eukaryotes, and their metabolism plays a key role in cellular energy balance, lipid homeostasis, growth, and maintenance. Plants accumulate oils primarily in seeds and fruits. Plant oils are used for food and feed and, increasingly, as feedstocks for biodiesel and industrial chemicals. Although plant vegetative tissues do not accumulate significant levels of triacylglycerols, they possess a high capacity for their synthesis, storage, and metabolism...
April 29, 2016: Annual Review of Plant Biology
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