@MicroGap

Bacterial signaling, c-di-GMP, c-di-AMP, protein domains NCBI's Comp. Bio. Branch, COG database, J. Bacteriology

 Bethesda, MD
Joined May 2016
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10Media
Cyanobacterial RNA-binding protein Asl3888 is ribosome-associated and involved in C/N metabolism. It is encoded in almost all cyanobacteria, green, red, and brown algae, diatoms, cryptomonads, and pelagophytes. biorxiv.org/content/10.64898…
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Чёрт, вся моя молодость прошла под эту музыку (позывные Русской службы Би-Би-Си) youtube.com/watch?v=z1088E6E…

Jeremiah Clarke - The Prince of Denmark's March (Lovely Rendition)

The Prince of Denmark's March, or commonly known as the Trumpet Vol...

youtube.com
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Very impressive: Novel myo-inositol to butyrate fermentation pathway in the prevalent human gut species Dysosmobacter welbionis, a bacterium associated with improved metabolic and liver health gut.bmj.com/content/early/20…
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Michael Galperin retweeted
Lee Harris
@LeeHarris18 Oct 2025
I can't believe what I've just watched. A Jewish lawyer wearing a Star of David was arrested after the police alleged the symbol had "antagonised" pro-Palestine protesters. He was handcuffed and detained by police for almost TEN hours. DISGUSTING! Shame on you @metpoliceuk.
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A new kind of magic mushroom: Two fungal genera use two distinct pathways to synthesize psilocybin onlinelibrary.wiley.com/doi/…

Dissimilar Reactions and Enzymes for Psilocybin Biosynthesis in Inocybe and Psilocybe Mushrooms

Mushrooms have learned twice independently how to make the iconic magic mushroom natural product psilocybin. This article introduces the enzymes of the second pathway, found in a fiber cap mushroom....

onlinelibrary.wiley.com
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FWIW: New mechanisms for bacterial motility and DNA transfer between bacteria decoded, via @EurekAlert! eurekalert.org/news-releases…

New mechanisms for bacterial motility and DNA transfer between bacteria decoded

Bacteria are constantly moving by help of motility organs called flagella or pili to colonize new niches. Also, bacteria can exchange information, like “speaking to each other”, and thus acquire new...

eurekalert.org
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Over two years in the making, but here it is: ComFB, the third family of c-di-GMP receptor proteins with representatives in multiple bacterial phyla (PMID: 40966295) doi.org/10.1073/pnas.2513041…

ComFB, a widespread family of c-di-NMP receptor proteins | PNAS

Cyclic dimeric-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that regulates a variety of cellular processes, including motility, biofil...

pnas.org
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Michael Galperin retweeted
Wiep Klaas Smits@SmitsLab12 Sep 2025
Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacteriology journals.asm.org/doi/10.1128…

Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacter...

Clostridioides difficile is an opportunistic pathogen for which better antibiotics are sorely needed. Most antibiotics target pathways that are essential for viability. Here, we use saturation...

journals.asm.org
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Some thoughts on metabolism and metabolic pathway holes pnas.org/doi/10.1073/pnas.25….

Using bioinformatics for identifying and plugging metabolic pathway holes | PNAS

Using bioinformatics for identifying and plugging metabolic pathway holes

pnas.org
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Lara Amorim, Conceição Santos and Kenneth Timmis Prioritising Microbiology in Secondary Education Addresses Emerging Scientific-Social-Educational Challenges and Competency Needs enviromicro-journals.onlinel…
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Michael Galperin retweeted
Chris Hendel@chrishendel1 Aug 2025
Incredible! Fascinating piece by Elisabeth Bik @MicrobiomDigest Discontinuous ridiculous stools – a preprint full of tortured phrases and stolen data scienceintegritydigest.com/2… h/t @RetractionWatch

Discontinuous ridiculous stools – a preprint full of tortured phrases and stolen data

“Patients with provocative entrail illness unclassified gave to crisis division a 3-day history of sickness, retching, migraine and irregular stomach torment alongside discontinuous ridiculous stoo…

scienceintegritydigest.com
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The interactions of c-di-GMP with the acidic residues seen in the MshEN domain could be quite widespread onlinelibrary.wiley.com/doi/… Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes

Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and...

The highly negatively charged phosphodiester groups of nucleic acids and cyclic (di-)nucleotides often interact with amino acids containing polar or positively charged sidechains. Due to charge...

onlinelibrary.wiley.com
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An interesting discussion: c-di-GMP does not bind H-NS, nor inhibits H-NS binding DNA | Nat. Comm nature.com/articles/s41467-0… (PMID: 40506437) Reply to: “c-di-GMP does not bind H-NS, nor inhibits H-NS binding DNA” | Nat. Comm nature.com/articles/s41467-0… (PMID: 40506445)
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Lee Kroos et al. (17 authors) From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology journals.asm.org/doi/full/10…

Milestones in the development of Myxococcus xanthus as a model multicellular bacterium | Journal of...

Myxobacteria are diverse, rod-shaped Gram-negative bacteria found in terrestrial and aquatic environments worldwide (1). A major claim to fame of these microorganisms is that the life cycle of...

journals.asm.org
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Michael Galperin retweeted
anna brogan@apbrogan17 Jun 2025
Very happy to share that a large part of my thesis work is out today: B. subtilis uses the second messenger c-di-AMP to modulate its turgor pressure in response to the state of its cell envelope.  nature.com/articles/s41564-0…
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In the architecture of the outer membrane complex PelBC for Pel export, the essential periplasmic ring of twelve PelC lipoproteins is mounted on top of the PelB β-barrel nature.com/articles/s41467-0…

Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas...

Nature Communications - The pathogen Pseudomonas aeruginosa uses a membrane complex, PelBC, to produce exopolysaccharides for biofilm formation. Here the authors combine structural analysis,...

nature.com
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In Bacillus subtilis, c-di-AMP levels are modulated by the cyclase regulator CdaR in response to cell wall defects. Great work by @apbrogan.bsky.social et al. nature.com/articles/s41564-0…
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This paper offers a solution to a long-standing problem: A general mechanism for initiating the bacterial general stress response | eLife @nielsbradshaw doi.org/10.7554/eLife.100376…

A general mechanism for initiating the bacterial general stress response

A coiled-coil-based transduction mechanism is identified for a serine/threonine phosphatase that controls a bacterial stress response, suggesting that phosphatases are part of a modularly exchangea...

elifesciences.org
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Michael Galperin retweeted
Khaled A. Selim@Selim_Khaled_11 Apr 2025
We cracked the mystery: Pteridines are the natural ligands of CutA, a widespread protein in nature @HHU_de @CoE_CMFI I started this project 8y ago. We showed that it's of PII signaling family, but it's role remained unknown coz we didn't know what it bind biorxiv.org/content/10.1101/…

Native metabolomics identifies pteridines as CutA ligands and modulators of copper binding

CutA, a conserved protein across all domains of life, has long been linked to copper tolerance in Escherichia coli , though recent studies question this association. To clarify its function, we...

biorxiv.org
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Novel families of selenoproteins journals.asm.org/doi/10.1128…

Novel selenoprotein neighborhoods suggest specialized biochemical processes | mSystems

Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast “dark matter” of hard-to-decipher protein sequences....

journals.asm.org
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