Emerging and divergent roles of pyrophosphorylated nucleotides in bacterial physiology and pathogenesis

Bacteria inhabit diverse environmental niches and consequently must modulate their metabolism to adapt to stress. The nucleotide second messengers guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) (collectively referred to as (p)ppGpp) are essential for survival during nutrient starvation. (p)ppGpp is synthesized by the RelA-SpoT homologue (RSH) protein family and coordinates the control of cellular metabolism through its combined effect on over 50 proteins. While the role of (p)ppGpp has largely been associated with nutrient limitation, recent studies have shown that (p)ppGpp and related nucleotides have a previously underappreciated effect on different aspects of bacterial physiology, such as maintaining cellular homeostasis and regulating bacterial interactions with a host, other bacteria, or phages. (p)ppGpp produced by pathogenic bacteria facilitates the evasion of host defenses such as reactive nitrogen intermediates, acidic pH, and the complement system. Additionally, (p)ppGpp and pyrophosphorylated derivatives of canonical adenosine nucleotides called (p)ppApp are emerging as effectors of bacterial toxin proteins. Here, we review the RSH protein family with a focus on its unconventional roles during host infection and bacterial competition.

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RNA Regulated Toxin-Antitoxin Systems in Pathogenic Bacteria

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.661026 ◽

2021 ◽

Vol 11 ◽

Author(s):

David D. Sarpong ◽

Erin R. Murphy

Keyword(s):

Small Rnas ◽

Pathogenic Bacteria ◽

Molecular Mechanisms ◽

Environmental Changes ◽

Bacterial Toxin ◽

Type I ◽

Bacterial Physiology ◽

Type Iii ◽

Two Factors

The dynamic host environment presents a significant hurdle that pathogenic bacteria must overcome to survive and cause diseases. Consequently, these organisms have evolved molecular mechanisms to facilitate adaptation to environmental changes within the infected host. Small RNAs (sRNAs) have been implicated as critical regulators of numerous pathways and systems in pathogenic bacteria, including that of bacterial Toxin-Antitoxin (TA) systems. TA systems are typically composed of two factors, a stable toxin, and a labile antitoxin which functions to protect against the potentially deleterious activity of the associated toxin. Of the six classes of bacterial TA systems characterized to date, the toxin component is always a protein. Type I and Type III TA systems are unique in that the antitoxin in these systems is an RNA molecule, whereas the antitoxin in all other TA systems is a protein. Though hotly debated, the involvement of TA systems in bacterial physiology is recognized by several studies, with the Type II TA system being the most extensively studied to date. This review focuses on RNA-regulated TA systems, highlighting the role of Type I and Type III TA systems in several pathogenic bacteria.

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(p)ppGpp-dependent regulation of the nucleotide hydrolase PpnN confers complement resistance in Salmonella enterica serovar Typhimurium

Infection and Immunity ◽

10.1128/iai.00639-20 ◽

2020 ◽

Author(s):

N. Y Elizabeth Chau ◽

Deyanira Pérez-Morales ◽

Wael Elhenawy ◽

Víctor H. Bustamante ◽

Yong E. Zhang ◽

...

Keyword(s):

Salmonella Enterica ◽

Pathogenic Bacteria ◽

Stringent Response ◽

Metabolic Reprogramming ◽

Bacterial Survival ◽

Complement Resistance ◽

Serovar Typhimurium ◽

Bacterial Fitness ◽

Host Infection

The stringent response is an essential mechanism of metabolic reprogramming during environmental stress that is mediated by the nucleotide alarmones, guanosine tetraphosphate and pentaphosphate ((p)ppGpp). In addition to physiological adaptations, (p)ppGpp also regulates virulence programs in pathogenic bacteria including Salmonella enterica serovar Typhimurium. S. Typhimurium is a common cause of acute gastroenteritis, but it may also spread to systemic tissues resulting in severe clinical outcomes. During infection, S. Typhimurium encounters a broad repertoire of immune defenses that it must evade for successful host infection. Here, we examined the role of the stringent response in S. Typhimurium resistance to complement-mediated killing and found that the (p)ppGpp synthetase-hydrolase, SpoT, is required for bacterial survival in human serum. We identified the nucleotide hydrolase, PpnN, as a target of the stringent response that is required to promote bacterial fitness in serum. Using chromatography and mass spectrometry, we show that PpnN hydrolyzes purine and pyrimidine monophosphates to generate free nucleobases and ribose 5′-phosphate, and that this metabolic activity is required for conferring resistance to complement killing. In addition to PpnN, we show that (p)ppGpp is required for the biosynthesis of the very long and long O-antigen in the outer membrane known to be important for complement resistance. Our results provide new insights into the role of the stringent response in mediating evasion of the innate immune system by pathogenic bacteria.

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A Toxin Involved inSalmonellaPersistence Regulates Its Activity by Acetylating Its Cognate Antitoxin, a Modification Reversed by CobB Sirtuin Deacetylase

mBio ◽

10.1128/mbio.00708-17 ◽

2017 ◽

Vol 8 (3) ◽

Cited By ~ 19

Author(s):

Chelsey M. VanDrisse ◽

Anastacia R. Parks ◽

Jorge C. Escalante-Semerena

Keyword(s):

Protein Synthesis ◽

Pathogenic Bacteria ◽

Bacterial Toxin ◽

Host Defenses ◽

Mobility Shift ◽

Reverse Transcription Pcr ◽

Acetylation State ◽

Host Infection

ABSTRACTBacterial toxin-antitoxin systems trigger the onset of a persister state by inhibiting essential cellular processes. The TacT toxin ofSalmonella entericais known to induce a persister state in macrophages through the acetylation of aminoacyl-tRNAs. Here, we show that the TacT toxin and the TacA antitoxin work as a complex that modulates TacT activity via the acetylation state of TacA. TacT acetylates TacA at residue K44, a modification that is removed by the NAD+-dependent CobB sirtuin deacetylase. TacA acetylation increases the activity of TacT, downregulating protein synthesis. TacA acetylation altered binding to its own promoter, although this did not changetacATexpression levels. These claims are supported by results fromin vitroprotein synthesis experiments used to monitor TacT activity,in vivogrowth analyses, electrophoretic mobility shift assays, and quantitative reverse transcription-PCR (RT-qPCR) analysis. TacT is the first example of a Gcn5-relatedN-acetyltransferase that modifies nonprotein and protein substrates.IMPORTANCEDuring host infection, pathogenic bacteria can modulate their physiology to evade host defenses. Some pathogens use toxin-antitoxin systems to modulate a state of self-toxicity that can decrease their cellular activity, triggering the onset of a persister state. The lower metabolic activity of persister cells allows them to escape host defenses and antibiotic treatments. Hence a better understanding of the mechanisms used by pathogens to ingress and egress the persister state is of relevance to human health.

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Type VI Secretion Systems of Erwinia amylovora Contribute to Bacterial Competition, Virulence, and Exopolysaccharide Production

Phytopathology ◽

10.1094/phyto-11-16-0393-r ◽

2017 ◽

Vol 107 (6) ◽

pp. 654-661 ◽

Cited By ~ 8

Author(s):

Yanli Tian ◽

Yuqiang Zhao ◽

Linye Shi ◽

Zhongli Cui ◽

Baishi Hu ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Erwinia Amylovora ◽

Antibacterial Activities ◽

Type Vi Secretion System ◽

Secretion Systems ◽

Pear Fruit ◽

Exopolysaccharide Production ◽

Bacterial Competition ◽

Type Vi Secretion

The type VI secretion system (T6SS) plays a major role in mediating interbacterial competition and might contribute to virulence in plant pathogenic bacteria. However, the role of T6SS in Erwinia amylovora remains unknown. In this study, 33 deletion mutants within three T6SS clusters were generated in E. amylovora strain NCPPB1665. Our results showed that all 33 mutants displayed reduced antibacterial activities against Escherichia coli as compared with that of the wild-type (WT) strain, indicating that Erwinia amylovora T6SS are functional. Of the 33 mutants, 19 exhibited reduced virulence on immature pear fruit as compared with that of the WT strain. Among them, 6, 1, and 12 genes belonged to T6SS-1, T6SS-2, and T6SS-3 clusters, respectively. Interestingly, these 19 mutants also produced less amylovoran or levan or both. These findings suggest that E. amylovora T6SS play a role in bacterial competition and virulence possibly by influencing exopolysaccharide production.

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Reviewing the role of peptide rarity in bacterial toxin immunomics

Frontiers in Bioscience ◽

10.2741/s263 ◽

2012 ◽

Vol S4 (1) ◽

pp. 216-225 ◽

Cited By ~ 1

Author(s):

Darja Kanduc

Keyword(s):

Bacterial Toxin

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Bioenhancing Effect of Cow Urine Distillate and Pepper Extract on Antibacterial Activity of Azadirachta Indica Leaves

International Journal of Pharmaceutical Sciences and Nanotechnology ◽

10.37285/ijpsn.2016.9.2.8 ◽

1970 ◽

Vol 9 (2) ◽

pp. 3212-3214

Author(s):

Pramod Dhakal ◽

Ankit a Achary ◽

Vedamurthy Joshi

Keyword(s):

Antibacterial Activity ◽

Azadirachta Indica ◽

Pathogenic Bacteria ◽

Ethanol Extract ◽

Watery Diarrhea ◽

Diffusion Method ◽

E Coli ◽

Drug Molecules ◽

Cow Urine

Bioenhancers are drug facilitator which do not show the typical drug activity but in combination to enhance the activity of other molecule in several way including increase the bioavailability of drug across the membrane, potentiating the drug molecules by conformational interaction, acting as receptor for drug molecules and making target cell more receptive to drugs and promote and increase the bioactivity or bioavailability or the uptake of drugs in combination therapy. The objective of the present study was to evaluate the antibacterial and activity of combination in Azadirachta indica extract with cow urine distillate and pepper extract against common pathogenic bacteria, a causative agent of watery diarrhea. It has been found that Indian indigenous cow urine and its distillate also possess bioenhancing ability. Bioenhancing role of cow urine distillate (CUD) and pepper extract was investigated on antibacterial activity of ethanol extract of Azadirachta indica. Antibacterial activity of ethanol extract neem alone and in combination with CUD and pepper extract were determined the ATCC strains against Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa and E-coli by cup plate diffusion method. Ethanol extract of neem has showed more effect on P. aeruginosa, E-coli than S. aureus and K. pneumonia with combination of CUD and pepper extract. CUD and pepper did not show any inhibition of test bacteria in low concentration. The antibacterial effect of combination of extract and CUD was higher than the inhibition caused by extract alone and is suggestive of the bioenhancing role of cow urine distillate and pepper. Moreover, inhibition of test bacteria was observed with less concentration of extract on combining with CUD

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The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis

Cells ◽

10.3390/cells10051083 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1083

Author(s):

Adhirath Sikand ◽

Malgorzata Jaszczur ◽

Linda B. Bloom ◽

Roger Woodgate ◽

Michael M. Cox ◽

...

Keyword(s):

Dna Synthesis ◽

Dna Polymerase ◽

Pathogenic Bacteria ◽

Fold Increase ◽

Translesion Dna Synthesis ◽

Sliding Clamp ◽

Pol V ◽

Dna Polymerase V ◽

Acting In Concert

In the mid 1970s, Miroslav Radman and Evelyn Witkin proposed that Escherichia coli must encode a specialized error-prone DNA polymerase (pol) to account for the 100-fold increase in mutations accompanying induction of the SOS regulon. By the late 1980s, genetic studies showed that SOS mutagenesis required the presence of two “UV mutagenesis” genes, umuC and umuD, along with recA. Guided by the genetics, decades of biochemical studies have defined the predicted error-prone DNA polymerase as an activated complex of these three gene products, assembled as a mutasome, pol V Mut = UmuD’2C-RecA-ATP. Here, we explore the role of the β-sliding processivity clamp on the efficiency of pol V Mut-catalyzed DNA synthesis on undamaged DNA and during translesion DNA synthesis (TLS). Primer elongation efficiencies and TLS were strongly enhanced in the presence of β. The results suggest that β may have two stabilizing roles: its canonical role in tethering the pol at a primer-3’-terminus, and a possible second role in inhibiting pol V Mut’s ATPase to reduce the rate of mutasome-DNA dissociation. The identification of umuC, umuD, and recA homologs in numerous strains of pathogenic bacteria and plasmids will ensure the long and productive continuation of the genetic and biochemical journey initiated by Radman and Witkin.

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Exploring Mucin as Adjunct to Phage Therapy

Microorganisms ◽

10.3390/microorganisms9030509 ◽

2021 ◽

Vol 9 (3) ◽

pp. 509

Author(s):

Amanda Carroll-Portillo ◽

Henry C. Lin

Keyword(s):

Pathogenic Bacteria ◽

Structural Changes ◽

Phage Therapy ◽

Bacterial Species ◽

Gi Tract ◽

Beneficial Bacteria ◽

Phage Cocktail ◽

Small Intestinal ◽

Gastrointestinal Dysbiosis

Conventional phage therapy using bacteriophages (phages) for specific targeting of pathogenic bacteria is not always useful as a therapeutic for gastrointestinal (GI) dysfunction. Complex dysbiotic GI disorders such as small intestinal bowel overgrowth (SIBO), ulcerative colitis (UC), or Crohn’s disease (CD) are even more difficult to treat as these conditions have shifts in multiple populations of bacteria within the microbiome. Such community-level structural changes in the gut microbiota may require an alternative to conventional phage therapy such as fecal virome transfer or a phage cocktail capable of targeting multiple bacterial species. Additionally, manipulation of the GI microenvironment may enhance beneficial bacteria–phage interactions during treatment. Mucin, produced along the entire length of the GI tract to protect the underlying mucosa, is a prominent contributor to the GI microenvironment and may facilitate bacteria–phage interactions in multiple ways, potentially serving as an adjunct during phage therapy. In this review, we will describe what is known about the role of mucin within the GI tract and how its facilitation of bacteria–phage interactions should be considered in any effort directed at optimizing effectiveness of a phage therapy for gastrointestinal dysbiosis.

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Special Issue: The Role of Complement in Cancer Immunotherapy

Antibodies ◽

10.3390/antib10030029 ◽

2021 ◽

Vol 10 (3) ◽

pp. 29

Author(s):

Ronald P. Taylor

Keyword(s):

Cancer Immunotherapy ◽

Complement System ◽

Immune Defense ◽

Special Issue ◽

The Complement System ◽

Critical Aspects

The complement system plays an important role in critical aspects of immune defense and in the maintenance of homeostasis in the bloodstream, as well as in essentially all tissues and organs [...]

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Ca2+ Microdomains, Calcineurin and the Regulation of Gene Transcription

Cells ◽

10.3390/cells10040875 ◽

2021 ◽

Vol 10 (4) ◽

pp. 875

Author(s):

Gerald Thiel ◽

Tobias Schmidt ◽

Oliver G. Rössler

Keyword(s):

Transcription Factors ◽

Protein Kinase ◽

Protein Kinases ◽

Gene Transcription ◽

Intracellular Signaling ◽

Second Messengers ◽

Major Function ◽

Surface Receptors ◽

Dependent Protein

Ca2+ ions function as second messengers regulating many intracellular events, including neurotransmitter release, exocytosis, muscle contraction, metabolism and gene transcription. Cells of a multicellular organism express a variety of cell-surface receptors and channels that trigger an increase of the intracellular Ca2+ concentration upon stimulation. The elevated Ca2+ concentration is not uniformly distributed within the cytoplasm but is organized in subcellular microdomains with high and low concentrations of Ca2+ at different locations in the cell. Ca2+ ions are stored and released by intracellular organelles that change the concentration and distribution of Ca2+ ions. A major function of the rise in intracellular Ca2+ is the change of the genetic expression pattern of the cell via the activation of Ca2+-responsive transcription factors. It has been proposed that Ca2+-responsive transcription factors are differently affected by a rise in cytoplasmic versus nuclear Ca2+. Moreover, it has been suggested that the mode of entry determines whether an influx of Ca2+ leads to the stimulation of gene transcription. A rise in cytoplasmic Ca2+ induces an intracellular signaling cascade, involving the activation of the Ca2+/calmodulin-dependent protein phosphatase calcineurin and various protein kinases (protein kinase C, extracellular signal-regulated protein kinase, Ca2+/calmodulin-dependent protein kinases). In this review article, we discuss the concept of gene regulation via elevated Ca2+ concentration in the cytoplasm and the nucleus, the role of Ca2+ entry and the role of enzymes as signal transducers. We give particular emphasis to the regulation of gene transcription by calcineurin, linking protein dephosphorylation with Ca2+ signaling and gene expression.

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