Long-Distance Transported RNAs: From Identity to Function

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Julia Kehr ◽  
Richard J. Morris ◽  
Friedrich Kragler
Keyword(s):  
Biological Function ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Messenger Rnas ◽  
Biological Functions ◽  
Long Distance ◽  
Rna Molecules ◽  
Open Questions ◽  
Different Types

There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether these RNAs are selected for transport and, if so, how they are selected and transported remain, in general, open questions. This aspect is likely not independent of the biological function and relevance of the transported RNAs, which are in most cases still unclear. In this review, we summarize the experimental data supporting selectivity or nonselectivity of RNA translocation and review the evidence for biological functions. After discussing potential issues regarding the comparability between experiments, we propose criteria that need to be critically evaluated to identify important signaling RNAs. Expected final online publication date for the Annual Review of Plant Biology, Volume 73 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PI(4,5)P2 Clustering and Its Impact on Biological Functions

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Yi Wen ◽  
Volker M. Vogt ◽  
Gerald W. Feigenson
Keyword(s):  
Plasma Membrane ◽  
Cell Biology ◽  
Cellular Proteins ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Cellular Functions ◽  
Dynamic Distribution ◽  
Multivalent Cation ◽  
Lipid Environment

Located at the inner leaflet of the plasma membrane, phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] comprises only 1–2 mol% of total PM lipids. With its synthesis and turnover both spatially and temporally regulated, PI(4,5)P2 recruits and interacts with hundreds of cellular proteins to support a broad spectrum of cellular functions. Several factors contribute to the versatile and dynamic distribution of PI(4,5)P2 in membranes. Physiological multivalent cations such as Ca2+ and Mg2+ can bridge between PI(4,5)P2 headgroups, forming nanoscopic PI(4,5)P2–cation clusters. The distinct lipid environment surrounding PI(4,5)P2 affects the degree of PI(4,5)P2 clustering. In addition, diverse cellular proteins interacting with PI(4,5)P2 can further regulate PI(4,5)P2 lateral distribution and accessibility. This review summarizes the current understanding of PI(4,5)P2 behavior in both cells and model membranes, with emphasis on both multivalent cation– and protein-induced PI(4,5)P2 clustering. Understanding the nature of spatially separated pools of PI(4,5)P2 is fundamental to cell biology. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Ecology and Evolution of Model Microbial Mutualisms

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jeremy M. Chacón ◽  
Sarah P. Hammarlund ◽  
Jonathan N.V. Martinson ◽  
Leno B. Smith ◽  
William R. Harcombe
Keyword(s):  
Future Study ◽  
Evolutionary Dynamics ◽  
Interspecific Interactions ◽  
Natural World ◽  
Annual Review ◽  
Publication Date ◽  
Controlled Experiments ◽  
Evolutionary Origins ◽  
Ecological Features ◽  
Open Questions

Mutually beneficial interspecific interactions are abundant throughout the natural world, including between microbes. Mutualisms between microbes are critical for everything from human health to global nutrient cycling. Studying model microbial mutualisms in the laboratory enables highly controlled experiments for developing and testing evolutionary and ecological hypotheses. In this review, we begin by describing the tools available for studying model microbial mutualisms. We then outline recent insights that laboratory systems have shed on the evolutionary origins, evolutionary dynamics, and ecological features of microbial mutualism. We touch on gaps in our current understanding of microbial mutualisms, note connections to mutualism in nonmicrobial systems, and call attention to open questions ripe for future study. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Zane Duxbury ◽  
Chih-hang Wu ◽  
Pingtao Ding
Keyword(s):  
Immune Responses ◽  
Genetic Architecture ◽  
Pathogen Detection ◽  
Current Knowledge ◽  
Plant Immunity ◽  
Innate Immune ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Nucleotide Binding Domain

Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Role of the Inflammasome in Liver Disease

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Marcelle de Carvalho Ribeiro ◽  
Gyongyi Szabo
Keyword(s):  
Liver Disease ◽  
Liver Diseases ◽  
Annual Review ◽  
Publication Date ◽  
Inflammasome Activation ◽  
Proinflammatory Response ◽  
Nonalcoholic Fatty Liver ◽  
Pyrin Domain ◽  
Different Types

The involvement of inflammasomes in the proinflammatory response observed in chronic liver diseases, such as alcohol-associated liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), is widely recognized. Although there are different types of inflammasomes, most studies to date have given attention to NLRP3 (nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3) in the pathogenesis of ALD, NAFLD/nonalcoholic steatohepatitis, and fibrosis. Canonical inflammasomes are intracellular multiprotein complexes that are assembled after the sensing of danger signals and activate caspase-1, which matures interleukin (IL)-1β, IL-18, and IL-37 and also induces a form of cell death called pyroptosis. Noncanonical inflammasomes activate caspase-11 to induce pyroptosis. We discuss the different types of inflammasomes involved in liver diseases with a focus on ( a) signals and mechanisms of inflammasome activation, ( b) the role of different types of inflammasomes and their products in the pathogenesis of liver diseases, and ( c) potential therapeutic strategies targeting components of the inflammasomes or cytokines produced upon inflammasome activation. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Mineral formation induced by cable bacteria performing long-distance electron transport in marine sediments

2018 ◽  
Author(s):  
Nicole M. J. Geerlings ◽  
Eva-Maria Zetsche ◽  
Silvia Hidalgo Martinez ◽  
Jack J. Middelburg ◽  
Filip J. R. Meysman
Keyword(s):  
Mineral Dissolution ◽  
Precipitation Process ◽  
Spectroscopic Techniques ◽  
Electron Microscopic ◽  
Long Distance ◽  
Direct Role ◽  
Clay Particles ◽  
Open Questions ◽  
Filamentous Microorganisms ◽  
Different Types

Abstract. Cable bacteria are multicellular, filamentous microorganisms that are capable of transporting electrons over centimeter-scale distances. Although recently discovered, these bacteria appear to be widely present in the seafloor, and when active, they exert a strong imprint on the local geochemistry. In particular, their electrogenic metabolism induces unusually strong pH excursions in aquatic sediments, which induces considerable mineral dissolution, and subsequent mineral re-precipitation. However at present, it is unknown whether and how cable bacteria play an active or direct role in the mineral re-precipitation process. To this end we present an explorative study of the formation of sedimentary minerals in and near filamentous cable bacteria using a combined approach of electron microscopic and spectroscopic techniques. Our observations reveal three different types of biomineral formation directly associated with cable bacteria: (1) the formation of intracellular polyphosphate granules, which are associated with a localized accumulation of calcium and magnesium, (2) the attachment and incorporation of clay particles in a sheath surrounding the surface of the cable bacterium filaments, and (3) the encrustation of cable bacteria filaments by newly formed solid phases containing high amounts of iron. These findings suggest a complex interaction between cable bacteria and the surrounding sediment matrix, and a substantial imprint of the electrogenic metabolism on mineral diagenesis and sedimentary biogeochemical cycling. Particularly the encrustation process leaves many open questions for further research. For example, we hypothesize that the complete encrustation of filaments might create a diffusion barrier and negatively impact the metabolism of the cable bacteria.

scholarly journals Mineral formation induced by cable bacteria performing long-distance electron transport in marine sediments

2019 ◽  
Vol 16 (3) ◽  
pp. 811-829 ◽  
Author(s):  
Nicole M. J. Geerlings ◽  
Eva-Maria Zetsche ◽  
Silvia Hidalgo-Martinez ◽  
Jack J. Middelburg ◽  
Filip J. R. Meysman
Keyword(s):  
Cell Envelope ◽  
Mineral Dissolution ◽  
Spectroscopic Techniques ◽  
Long Distance ◽  
Direct Role ◽  
Clay Particles ◽  
Explorative Study ◽  
Open Questions ◽  
Filamentous Microorganisms ◽  
Different Types

Abstract. Cable bacteria are multicellular, filamentous microorganisms that are capable of transporting electrons over centimeter-scale distances. Although recently discovered, these bacteria appear to be widely present in the seafloor, and when active they exert a strong imprint on the local geochemistry. In particular, their electrogenic metabolism induces unusually strong pH excursions in aquatic sediments, which induces considerable mineral dissolution, and subsequent mineral reprecipitation. However, at present, it is unknown whether and how cable bacteria play an active or direct role in the mineral reprecipitation process. To this end we present an explorative study of the formation of sedimentary minerals in and near filamentous cable bacteria using a combined approach of electron microscopy and spectroscopic techniques. Our observations reveal the formation of polyphosphate granules within the cells and two different types of biomineral formation directly associated with multicellular filaments of these cable bacteria: (i) the attachment and incorporation of clay particles in a coating surrounding the bacteria and (ii) encrustation of the cell envelope by iron minerals. These findings suggest a complex interaction between cable bacteria and the surrounding sediment matrix, and a substantial imprint of the electrogenic metabolism on mineral diagenesis and sedimentary biogeochemical cycling. In particular, the encrustation process leaves many open questions for further research. For example, we hypothesize that the complete encrustation of filaments might create a diffusion barrier and negatively impact the metabolism of the cable bacteria.

Feruloylated Arabinoxylan and Oligosaccharides: Chemistry, Nutritional Functions, and Options for Enzymatic Modification

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shang Lin ◽  
Jane W. Agger ◽  
Casper Wilkens ◽  
Anne S. Meyer
Keyword(s):  
Cell Walls ◽  
Annual Review ◽  
Publication Date ◽  
Food Ingredients ◽  
Structural Modifications ◽  
Grain Processing ◽  
Cereal Grain ◽  
Different Types ◽  
Cereal Brans ◽  
Antioxidant Effects

Cereal brans and grain endosperm cell walls are key dietary sources of different types of arabinoxylan. Arabinoxylan is the main group of hemicellulosic polysaccharides that are present in the cell walls of monocot grass crops and hence in cereal grains. The arabinoxylan polysaccharides consist of a backbone of β-(1→4)-linked xylopyranosyl residues, which carry arabinofuranosyl moieties, hence the term arabinoxylan. Moreover, the xylopyranosyl residues can be acetylated or substituted by methyl-glucuronic acid. The arabinofuranosyls may be esterified with a feruloyl group. Feruloylated arabinoxylo-oligosaccharides exert beneficial bioactivities via prebiotic, immunomodulatory, and/or antioxidant effects. New knowledge on microbial enzymes that catalyze specific structural modifications of arabinoxylans can help us understand how these complex fibers are converted in the gut and provide a foundation for the production of feruloylated arabinoxylo-oligosaccharides from brans or other cereal grain processing sidestreams as functional food ingredients. There is a gap between the structural knowledge, bioactivity data, and enzymology insight. Our goal with this review is to present an overview of the structures and bioactivities of feruloylated arabinoxylo-oligosaccharides and review the enzyme reactions that catalyze specific changes in differentially substituted arabinoxylans. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 12 is March 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Plant Pan-Genomics Comes of Age

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Li Lei ◽  
Eugene Goltsman ◽  
David Goodstein ◽  
Guohong Albert Wu ◽  
Daniel S. Rokhsar ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Large Size ◽  
Sizable Fraction

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Making of Plant Armor: The Periderm

2022 ◽  
Vol 73 (1) ◽  
Author(s):  
Olga Serra ◽  
Ari Pekka Mähönen ◽  
Alexander J. Hetherington ◽  
Laura Ragni
Keyword(s):  
Regulatory Networks ◽  
Plant Biology ◽  
Raw Material ◽  
Industrial Processes ◽  
Annual Review ◽  
Publication Date ◽  
Biotic And Abiotic Stress ◽  
Meristematic Tissue ◽  
Future Challenges ◽  
Periderm Formation

The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO2. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research. Expected final online publication date for the Annual Review of Plant Biology, Volume 73 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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