Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Gert Bange ◽  
Ditlev E. Brodersen ◽  
Anastasia Liuzzi ◽  
Wieland Steinchen
Keyword(s):  
Second Messengers ◽  
Stringent Response ◽  
Direct Interaction ◽  
Growth Conditions ◽  
Annual Review ◽  
Publication Date ◽  
Cellular Processes ◽  
Gram Positive Bacteria ◽  
Downstream Effects ◽  
Structural Aspects

Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Diego O. Serra ◽  
Regine Hengge
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Second Messengers ◽  
Emergent Properties ◽  
Annual Review ◽  
Publication Date ◽  
Growth And Survival ◽  
Chemical Gradients ◽  
Life Itself ◽  
Scale Matrix

Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Measuring Absolute Membrane Potential Across Space and Time

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Julia R. Lazzari-Dean ◽  
Anneliese M.M. Gest ◽  
Evan W. Miller
Keyword(s):  
Membrane Potential ◽  
Neurotransmitter Release ◽  
Cell Cycle Control ◽  
The Other ◽  
Annual Review ◽  
Publication Date ◽  
Short Term ◽  
Cellular Processes ◽  
Sensing Platform ◽  
The One

Membrane potential (Vmem) is a fundamental biophysical signal present in all cells. Vmem signals range in time from milliseconds to days, and they span lengths from microns to centimeters. Vmem affects many cellular processes, ranging from neurotransmitter release to cell cycle control to tissue patterning. However, existing tools are not suitable for Vmem quantification in many of these areas. In this review, we outline the diverse biology of Vmem, drafting a wish list of features for a Vmem sensing platform. We then use these guidelines to discuss electrode-based and optical platforms for interrogating Vmem. On the one hand, electrode-based strategies exhibit excellent quantification but are most effective in short-term, cellular recordings. On the other hand, optical strategies provide easier access to diverse samples but generally only detect relative changes in Vmem. By combining the respective strengths of these technologies, recent advances in optical quantification of absolute Vmem enable new inquiries into Vmem biology. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Compositional, Structural, and Kinetic Aspects of Lipid Digestion and Bioavailability: In Vitro, In Vivo, and Modeling Approaches

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Sébastien Marze
Keyword(s):  
Annual Review ◽  
Publication Date ◽  
Lipid Digestion ◽  
Modeling Approaches ◽  
Digestion Kinetics ◽  
Food Design ◽  
Structural Aspects ◽  
Development And Evolution

Lipid digestion and bioavailability are usually investigated separately, using different approaches (in vitro, modeling, in vivo). However, a few inclusive studies show that their kinetics are closely linked. Lipid bioavailability kinetics is likely involved in the development and evolution of several diseases, so lipid digestion kinetics could be involved as well and can be modulated by food design or combination. To illustrate this possibility, the compositional and structural aspects of lipid digestion kinetics, as investigated using in vitro and modeling approaches, are presented first. Then, in vivo and mixed approaches enabling the study of both kinetics are reviewed and discussed. Finally, disparate modeling approaches are introduced, and a unifying modeling scheme is proposed, opening new perspectives for understanding the role and interactions of various factors (chemical, physical, and biological) involved in lipid metabolism. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The VapBC1 toxin–antitoxin complex fromMycobacterium tuberculosis: purification, crystallization and X-ray diffraction analysis

2016 ◽  
Vol 72 (6) ◽  
pp. 485-489 ◽  
Author(s):  
Zuokun Lu ◽  
Han Wang ◽  
Aili Zhang ◽  
Yusheng Tan
Keyword(s):  
Sparse Matrix ◽  
Stringent Response ◽  
Normal Growth ◽  
Growth Conditions ◽  
Biological Processes ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Cellular Processes ◽  
Crystallization Solution

Mycobacterium tuberculosis, a major human pathogen, encodes at least 88 toxin–antitoxin (TA) systems. Remarkably, more than half of these modules belong to the VapBC family. Under normal growth conditions, the toxicity of the toxin VapC is neutralized by the protein antitoxin VapB. When bacteria face an unfavourable environment, the antitoxin is degraded and the free toxin VapC targets important cellular processes in order to inhibit cell growth. TA systems function in many biological processes, such as in the stringent response, in biofilm formation and in drug tolerance. To explore the structure of the VapBC1 complex, the toxin VapC1 and the antitoxin VapB1 were separately cloned, co-expressed and crystallized. The best crystal was obtained using a crystallization solution consisting of optimized solution with commercial sparse-matrix screen solutions as additives. The crystal diffracted to a resolution of 2.7 Å and belonged to space groupP21, with unit-cell parametersa= 59.3,b= 106.7,c = 250.0 Å, β = 93.75°.

scholarly journals Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Rajarshi P. Ghosh ◽  
Barbara J. Meyer
Keyword(s):  
Single Molecule ◽  
Genome Organization ◽  
Spatial Organization ◽  
Super Resolution ◽  
Annual Review ◽  
Publication Date ◽  
Cellular Processes ◽  
Regulatory Processes ◽  
Genome Wide ◽  
Resolution Imaging

Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Quorum Sensing in Fungal Species

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Xiuyun Tian ◽  
Hao Ding ◽  
Weixin Ke ◽  
Linqi Wang
Keyword(s):  
Quorum Sensing ◽  
Cell Communication ◽  
Fungal Species ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Cellular Processes ◽  
Fungal Biology ◽  
Wide Range ◽  
Important Direction

Quorum sensing (QS) is one of the most studied cell-cell communication mechanisms in fungi. Research in the last 20 years has explored various fungal QS systems that are involved in a wide range of biological processes, especially eukaryote- or fungus-specific behaviors, mirroring the significant contribution of QS regulation to fungal biology and evolution. Based on recent progress, we summarize in this review fungal QS regulation, with an emphasis on its functional role in behaviors unique to fungi or eukaryotes. We suggest that using fungi as genetically amenable eukaryotic model systems to address why and how QS regulation is integrated into eukaryotic reproductive strategies and molecular or cellular processes could be an important direction for QS research. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Political Control

2021 ◽  
Vol 25 (1) ◽  
Author(s):  
Mai Hassan ◽  
Daniel Mattingly ◽  
Elizabeth R. Nugent
Keyword(s):  
Recent Literature ◽  
State Policies ◽  
Science Volume ◽  
Political Control ◽  
Annual Review ◽  
Publication Date ◽  
Political Leaders ◽  
Downstream Effects ◽  
Regime Types ◽  
Analytical Utility

Political leaders use different tactics to ensure widespread compliance with state policies and to minimize resistance. Scholarship tends to treat different tactics individually, suggesting fundamental dissimilarities in underpinning logic and goals. We introduce political control as a concept that unifies these different tactics within a single framework and demonstrate the analytical utility of considering seemingly disparate strategies in conversation rather than in isolation. We synthesize a growing recent literature on political control, including innovative approaches to repression as well as studies of indoctrination, distribution, and infiltration. We argue that tactics of political control can be understood to vary along two primary dimensions: the level of violence and the materiality of rewards. We highlight recent inquiry into the downstream effects of political control. We conclude with a call for more research on political control that considers combinations of different tactics, across regime types, in a world where tolerance of violent repression is diminishing. Expected final online publication date for the Annual Review of Political Science, Volume 25 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Elucidation of Gram-Positive Bacterial Iron(III) Reduction for Kaolinite Clay Refinement

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3084
Author(s):  
Hao Jing ◽  
Zhao Liu ◽  
Seng How Kuan ◽  
Sylvia Chieng ◽  
Chun Loong Ho
Keyword(s):  
Iron Reduction ◽  
Growth Conditions ◽  
Cellular Interaction ◽  
Kaolin Clay ◽  
Media Composition ◽  
Gram Positive ◽  
Kaolinite Clay ◽  
Gram Positive Bacteria ◽  
Rich Media ◽  
The Media

Recently, microbial-based iron reduction has been considered as a viable alternative to typical chemical-based treatments. The iron reduction is an important process in kaolin refining, where iron-bearing impurities in kaolin clay affects the whiteness, refractory properties, and its commercial value. In recent years, Gram-negative bacteria has been in the center stage of iron reduction research, whereas little is known about the potential use of Gram-positive bacteria to refine kaolin clay. In this study, we investigated the ferric reducing capabilities of five microbes by manipulating the microbial growth conditions. Out of the five, we discovered that Bacillus cereus and Staphylococcus aureus outperformed the other microbes under nitrogen-rich media. Through the biochemical changes and the microbial behavior, we mapped the hypothetical pathway leading to the iron reduction cellular properties, and found that the iron reduction properties of these Gram-positive bacteria rely heavily on the media composition. The media composition results in increased basification of the media that is a prerequisite for the cellular reduction of ferric ions. Further, these changes impact the formation of biofilm, suggesting that the cellular interaction for the iron(III)oxide reduction is not solely reliant on the formation of biofilms. This article reveals the potential development of Gram-positive microbes in facilitating the microbial-based removal of metal contaminants from clays or ores. Further studies to elucidate the corresponding pathways would be crucial for the further development of the field.

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.

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