scholarly journals GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP

2015 ◽  
Vol 112 (17) ◽  
pp. 5383-5388 ◽  
Author(s):  
Colleen A. Kellenberger ◽  
Stephen C. Wilson ◽  
Scott F. Hickey ◽  
Tania L. Gonzalez ◽  
Yichi Su ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Cell Biology ◽  
Environmental Remediation ◽  
Geobacter Sulfurreducens ◽  
Extracellular Electron Transfer ◽  
Bacterial Physiology ◽  
Fluorescent Biosensor ◽  
Environmental Bacterium ◽  
Cyclic Dinucleotides ◽  
And Function

Cyclic dinucleotides are an expanding class of signaling molecules that control many aspects of bacterial physiology. A synthase for cyclic AMP-GMP (cAG, also referenced as 3′-5′, 3′-5′ cGAMP) called DncV is associated with hyperinfectivity of Vibrio cholerae but has not been found in many bacteria, raising questions about the prevalence and function of cAG signaling. We have discovered that the environmental bacterium Geobacter sulfurreducens produces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membranes, and Motility) as specific receptors for cAG. GEMM-Ib riboswitches regulate genes associated with extracellular electron transfer; thus cAG signaling may control aspects of bacterial electrophysiology. These findings expand the role of cAG beyond organisms that harbor DncV and beyond pathogenesis to microbial geochemistry, which is important to environmental remediation and microbial fuel cell development. Finally, we have developed an RNA-based fluorescent biosensor for live-cell imaging of cAG. This selective, genetically encodable biosensor will be useful to probe the biochemistry and cell biology of cAG signaling in diverse bacteria.

scholarly journals Microfluidic dielectrophoresis illuminates the relationship between microbial cell envelope polarizability and electrochemical activity

2019 ◽  
Vol 5 (1) ◽  
pp. eaat5664 ◽  
Author(s):  
Qianru Wang ◽  
A.-Andrew D. Jones ◽  
Jeffrey A. Gralnick ◽  
Liwei Lin ◽  
Cullen R. Buie
Keyword(s):  
Environmental Remediation ◽  
Cell Envelope ◽  
Shewanella Oneidensis ◽  
Growth Conditions ◽  
Geobacter Sulfurreducens ◽  
Rapid Screening ◽  
Extracellular Electron Transfer ◽  
Insoluble Electron Acceptors ◽  
The Relationship ◽  
Type Strains

Electrons can be transported from microbes to external insoluble electron acceptors (e.g., metal oxides or electrodes in an electrochemical cell). This process is known as extracellular electron transfer (EET) and has received considerable attention due to its applications in environmental remediation and energy conversion. However, the paucity of rapid and noninvasive phenotyping techniques hinders a detailed understanding of microbial EET mechanisms. Most EET phenotyping techniques assess microorganisms based on their metabolism and growth in various conditions and/or performance in electrochemical systems, which requires large sample volumes and cumbersome experimentation. Here, we use microfluidic dielectrophoresis to show a strong correlation between bacterial EET and surface polarizability. We analyzed surface polarizabilities for wild-type strains and cytochrome-deletion mutants of two model EET microbes,Geobacter sulfurreducensandShewanella oneidensis, and forEscherichia colistrains heterologously expressingS. oneidensisEET pathways in various growth conditions. Dielectrophoretic phenotyping is achieved with small cell culture volumes (~100 μl) in a short amount of time (1 to 2 min per strain). Our work demonstrates that cell polarizability is diminished in response to deletions of crucial outer-membrane cytochromes and enhanced due to additions of EET pathways. Results of this work hold exciting promise for rapid screening of direct EET or other cell envelope phenotypes using cell polarizability as a proxy, especially for microbes difficult to cultivate in laboratory conditions.

scholarly journals Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3′, 3′-cGAMP)

2016 ◽  
Vol 113 (7) ◽  
pp. 1790-1795 ◽  
Author(s):  
Zachary F. Hallberg ◽  
Xin C. Wang ◽  
Todd A. Wright ◽  
Beiyan Nan ◽  
Omer Ad ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Predictive Power ◽  
Geobacter Sulfurreducens ◽  
Bacterial Genomes ◽  
Diguanylate Cyclases ◽  
Genes Encoding ◽  
Cyclic Dinucleotides ◽  
Ggdef Domain ◽  
Cyclic Dinucleotide

Over 30 years ago, GGDEF domain-containing enzymes were shown to be diguanylate cyclases that produce cyclic di-GMP (cdiG), a second messenger that modulates the key bacterial lifestyle transition from a motile to sessile biofilm-forming state. Since then, the ubiquity of genes encoding GGDEF proteins in bacterial genomes has established the dominance of cdiG signaling in bacteria. However, the observation that proteobacteria encode a large number of GGDEF proteins, nearing 1% of coding sequences in some cases, raises the question of why bacteria need so many GGDEF enzymes. In this study, we reveal that a subfamily of GGDEF enzymes synthesizes the asymmetric signaling molecule cyclic AMP-GMP (cAG or 3′, 3′-cGAMP). This discovery is unexpected because GGDEF enzymes function as symmetric homodimers, with each monomer binding to one substrate NTP. Detailed analysis of the enzyme from Geobacter sulfurreducens showed it is a dinucleotide cyclase capable of switching the major cyclic dinucleotide (CDN) produced based on ATP-to-GTP ratios. We then establish through bioinformatics and activity assays that hybrid CDN-producing and promiscuous substrate-binding (Hypr) GGDEF enzymes are found in other deltaproteobacteria. Finally, we validated the predictive power of our analysis by showing that cAG is present in surface-grown Myxococcus xanthus. This study reveals that GGDEF enzymes make alternative cyclic dinucleotides to cdiG and expands the role of this widely distributed enzyme family to include regulation of cAG signaling.

The Effect of Mitomycin C on Platelet Aggregation and Adenosine 3′, 5′-Monophosphate Metabolism

1978 ◽  
Vol 39 (01) ◽  
pp. 177-185 ◽  
Author(s):  
Shuichi Hashimoto ◽  
Sachiko Shibata ◽  
Bonro Kobayashi
Keyword(s):  
Platelet Aggregation ◽  
Cyclic Amp ◽  
Mitomycin C ◽  
Blood Platelets ◽  
Adenosine Diphosphate ◽  
Cellular Membrane ◽  
Adenyl Cyclase ◽  
Cyclic Amp Phosphodiesterase ◽  
Membrane Structure And Function ◽  
And Function

SummaryThe effect of Mitomycin C on aggregation, adenosine 3′, 5′-monophosphate (cyclic AMP) metabolism and reactions induced by thrombin was studied in rabbit platelets. Mitomycin C inhibited the platelet aggregation induced by adenosine diphosphate or thrombin. The level of radioactive cyclic AMP derived from 8-14C adenine or 8-14C adenosine increased after incubating intact platelets with Mitomycin G. Formation of radioactive adenosine triphosphate also increased though mitochondrial oxidation was not stimulated. Similar effect was observed also in rabbit liver. Mitomycin C failed to stimulate platelet adenyl cyclase but inhibited cyclic AMP phosphodiesterase in the absence of theophylline. In the platelets preincubated with Mitomycin C, thrombin-induced inhibition of adenyl cyclase, stimulation of membrane-bound cyclic AMP phosphodiesterase, and release of 250,000 dalton protein from platelet membranes were prevented. These results suggest that Mitomycin C will affect cellular membrane structure and function, and this extranuclear effect of Mitomycin C will lead to inhibition of aggregation in blood platelets.

scholarly journals Membrane-associated phase separation: organization and function emerge from a two-dimensional milieu

2021 ◽  
Author(s):  
Jonathon A Ditlev
Keyword(s):  
Phase Separation ◽  
Cell Biology ◽  
Cellular Environment ◽  
Condensate Formation ◽  
Associated Proteins ◽  
Available Technology ◽  
And Function ◽  
Surrounding Membrane

Abstract Liquid‒liquid phase separation (LLPS) of biomolecules has emerged as an important mechanism that contributes to cellular organization. Phase separated biomolecular condensates, or membrane-less organelles, are compartments composed of specific biomolecules without a surrounding membrane in the nucleus and cytoplasm. LLPS also occurs at membranes, where both lipids and membrane-associated proteins can de-mix to form phase separated compartments. Investigation of these membrane-associated condensates using in vitro biochemical reconstitution and cell biology has provided key insights into the role of phase separation in membrane domain formation and function. However, these studies have generally been limited by available technology to study LLPS on model membranes and the complex cellular environment that regulates condensate formation, composition, and function. Here, I briefly review our current understanding of membrane-associated condensates, establish why LLPS can be advantageous for certain membrane-associated condensates, and offer a perspective for how these condensates may be studied in the future.

Tissue engineering in periodontics- A demystifing review

2021 ◽  
pp. 1-5
Author(s):  
Shivani Sachdeva ◽  
Harish Saluja ◽  
Amit Mani ◽  
M.B. Phadnaik
Keyword(s):  
Tissue Engineering ◽  
Tissue Regeneration ◽  
Cell Biology ◽  
Alveolar Bone ◽  
Complete Recovery ◽  
Medical Sciences ◽  
Alternative Approach ◽  
Periodontal Tissue Regeneration ◽  
Novel Concept ◽  
And Function

INTRODUCTION: Novel concept known as tissue engineering is for the betterment of human. The use of much advanced molecular science and cell biology in processing the tissues to regenerate even after the loss of inborn tendency of pluripotent cells to multiply is possible by this new therapy. CONTENT: Periodontal tissue regeneration in both height and function is attributed to a complete recovery of the periodontal structures, that is, the formation of alveolar bone, a new connective attachment through collagen fibers as well as functionally oriented on the newly formed cementum is regeneration. Cell based therapies including tissue regeneration is an alternative approach for the regeneration of tissues damaged by disease or trauma. SUMMARY: Though tissue engineering requires the fundamentals of all the three keys namely genomics, proteomics and biometrics to give the solutions to biological problems appearing in dentistry as well as medical sciences.

Geobacter sulfurreducens adapts to low electrode potential for extracellular electron transfer

2016 ◽  
Vol 191 ◽  
pp. 743-749 ◽  
Author(s):  
Luo Peng ◽  
Xiao-Ting Zhang ◽  
Jie Yin ◽  
Shuo-Yuan Xu ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electrode Potential ◽  
Geobacter Sulfurreducens ◽  
Extracellular Electron Transfer

Biological Phase Separation and Biomolecular Condensates in Plants

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Ryan J. Emenecker ◽  
Alex S. Holehouse ◽  
Lucia C. Strader
Keyword(s):  
Phase Separation ◽  
Cell Biology ◽  
Condensed Matter ◽  
Annual Review ◽  
Publication Date ◽  
Nuclear Speckles ◽  
The Past ◽  
Shared Property ◽  
And Function ◽  
Physical Principles

A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems. 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.

scholarly journals The Isoform Selective Roles of PI3Ks in Dendritic Cell Biology and Function

2018 ◽  
Vol 9 ◽  
Author(s):  
Ezra Aksoy ◽  
Loredana Saveanu ◽  
Bénédicte Manoury
Keyword(s):  
Dendritic Cell ◽  
Cell Biology ◽  
And Function

scholarly journals The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Jeremy T. Ritzert ◽  
George Minasov ◽  
Ryan Embry ◽  
Matthew J. Schipma ◽  
Karla J. F. Satchell
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Carbon Source ◽  
Cyclic Amp ◽  
Yersinia Pestis ◽  
Carbon Sources ◽  
Transcriptional Regulator ◽  
Receptor Protein ◽  
Content Type ◽  
Bacterial Physiology

ABSTRACT Cyclic AMP (cAMP) receptor protein (Crp) is an important transcriptional regulator of Yersinia pestis. Expression of crp increases during pneumonic plague as the pathogen depletes glucose and forms large biofilms within lungs. To better understand control of Y. pestis Crp, we determined a 1.8-Å crystal structure of the protein-cAMP complex. We found that compared to Escherichia coli Crp, C helix amino acid substitutions in Y. pestis Crp did not impact the cAMP dependency of Crp to bind DNA promoters. To investigate Y. pestis Crp-regulated genes during plague pneumonia, we performed RNA sequencing on both wild-type and Δcrp mutant bacteria growing in planktonic and biofilm states in minimal media with glucose or glycerol. Y. pestis Crp was found to dramatically alter expression of hundreds of genes in a manner dependent upon carbon source and growth state. Gel shift assays confirmed direct regulation of the malT and ptsG promoters, and Crp was then linked to Y. pestis growth on maltose as a sole carbon source. Iron regulation genes ybtA and fyuA were found to be indirectly regulated by Crp. A new connection between carbon source and quorum sensing was revealed as Crp was found to regulate production of acyl-homoserine lactones (AHLs) through direct and indirect regulation of genes for AHL synthetases and receptors. AHLs were subsequently identified in the lungs of Y. pestis-infected mice when crp expression was highest in Y. pestis biofilms. Thus, in addition to the well-studied pla gene, other Crp-regulated genes likely have important functions during plague infection. IMPORTANCE Bacterial pathogens have evolved extensive signaling pathways to translate environmental signals into changes in gene expression. While Crp has long been appreciated for its role in regulating metabolism of carbon sources in many bacterial species, transcriptional profiling has revealed that this protein regulates many other aspects of bacterial physiology. The plague pathogen Y. pestis requires this global regulator to survive in blood, skin, and lungs. During disease progression, this organism adapts to changes within these niches. In addition to regulating genes for metabolism of nonglucose sugars, we found that Crp regulates genes for virulence, metal acquisition, and quorum sensing by direct or indirect mechanisms. Thus, this single transcriptional regulator, which responds to changes in available carbon sources, can regulate multiple critical behaviors for causing disease.

scholarly journals Discovery of keratin function and role in genetic diseases: the year that 1991 was

2016 ◽  
Vol 27 (18) ◽  
pp. 2807-2810 ◽  
Author(s):  
Pierre A. Coulombe
Keyword(s):  
Intermediate Filaments ◽  
Cell Biology ◽  
Essential Role ◽  
Genetic Diseases ◽  
Structure And Function ◽  
Mechanical Support ◽  
25Th Anniversary ◽  
Keratin Filaments ◽  
And Function ◽  
Keratin Intermediate Filaments

In 1991, a set of transgenic mouse studies took the fields of cell biology and dermatology by storm in providing the first credible evidence that keratin intermediate filaments play a unique and essential role in the structural and mechanical support in keratinocytes of the epidermis. Moreover, these studies intimated that mutations altering the primary structure and function of keratin filaments underlie genetic diseases typified by cellular fragility. This Retrospective on how these studies came to be is offered as a means to highlight the 25th anniversary of these discoveries.

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