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1. Calmodulin‐binding transcription activator AtSR1 / CAMTA3 fine‐tunes plant immune response by transcriptional regulation of the salicylate receptor NPR1

   https://doi.org/10.1111/pce.14123  

   Yuan, Peiguo ; Tanaka, Kiwamu ; Poovaiah, B. W. ( June 2021 , Plant, Cell & Environment)

   Calcium (Ca²⁺) signalling regulates salicylic acid (SA)‐mediated immune response through calmodulin‐meditated transcriptional activators, AtSRs/CAMTAs, but its mechanism is not fully understood. Here, we report an AtSR1/CAMTA3‐mediated regulatory mechanism involving the expression of the SA receptor, NPR1. Results indicate that the transcriptional expression ofNPR1was regulated by AtSR1 binding to a CGCG box in theNPR1promotor. Theatsr1mutant exhibited resistance to the virulent strain ofPseudomonas syringaepv.tomato(Pst), however, was susceptible to an avirulentPststrain carryingavrRpt2, due to the failure of the induction of hypersensitive responses. These resistant/susceptible phenotypes in theatsr1mutant were reversed in thenpr1mutant background, suggesting that AtSR1 regulates NPR1 as a downstream target during plant immune response. The virulentPststrain triggered a transient elevation in intracellular Ca²⁺concentration, whereas the avirulentPststrain triggered a prolonged change. The distinct Ca²⁺signatures were decoded into the regulation of NPR1 expression through AtSR1's IQ motif binding with Ca²⁺‐free‐CaM2, while AtSR1's calmodulin‐binding domain with Ca²⁺‐bound‐CaM2. These observations reveal a role for AtSR1 as a Ca²⁺‐mediated transcription regulator in controlling the NPR1‐mediated plant immune response.

    

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2. Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin

   https://doi.org/10.1002/prot.26009  

   Raut, Priyam ; Glass, Jennifer B. ; Lieberman, Raquel L. ( October 2020 , Proteins: Structure, Function, and Bioinformatics)

   Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life. In addition to eukaryotes, IAPs are encoded in metabolically diverse archaea from a wide range of environments. We found three distinct clades of archaeal IAPs: (a)Euryarchaeota(eg, halophilicHalobacteriales, methanogenicMethanosarcinalesandMethanomicrobiales, marinePoseidoniales, acidophilicThermoplasmatales, hyperthermophilicArchaeoglobusspp.), (b) DPANN, and (c)Bathyarchaeota,Crenarchaeota, andAsgard. IAPs were also present in bacterial genomes from uncultivated members of Candidate Phylum Radiation, perhaps due to horizontal gene transfer from DPANN archaeal lineages. Sequence analysis of the catalytic motif YD…GXGD (where X is any amino acid) in IAPs from archaea and bacteria reveals WD inLokiarchaeotaand many residue types in the X position. Gene neighborhood analysis in halophilic archaea shows IAP genes near corrinoid transporters (btuCDFgenes). In marineEuryarchaeota, a putative BtuF‐like domain is found in N‐terminus of the IAP gene, suggesting a role for these IAPs in metal ion cofactor or other nutrient scavenging. Interestingly, eukaryotic IAP family members appear to have evolved either fromEuryarchaeotaor fromAsgardarchaea. Taken together, our phylogenetic and bioinformatics analysis should prompt experiments to probe the biological roles of IAPs in prokaryotic secretomes.

    

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3. Can ozone be used to calibrate aerosol photoacoustic spectrometers?

   https://doi.org/10.5194/amt-11-6419-2018  

   Fischer, D. Al ; Smith, Geoffrey D. ( January 2018 , Atmospheric Measurement Techniques)

   Abstract. Photoacoustic spectroscopy (PAS) has become a popular technique for measuringabsorption of light by atmospheric aerosols in both the laboratory andfield campaigns. It has low detection limits, measures suspended aerosols,and is insensitive to scattering. But PAS requires rigorous calibration to beapplied quantitatively. Often, a PAS instrument is either filled with a gasof known concentration and absorption cross section, such that the absorptionin the cell can be calculated from the product of the two, or the absorptionis measured independently with a technique such as cavity ring-downspectroscopy. Then, the PAS signal can be regressed upon the known absorptionto determine a calibration slope that reflects the sensitivity constant ofthe cell and microphone. Ozone has been used for calibrating PAS instrumentsdue to its well-known UV–visible absorption spectrum and the ease with whichit can be generated. However, it is known to photodissociate up toapproximately 1120nm via the O₃ + $h\mathit{\nu }(\>\mathrm{1.1}\mathrm{eV})\to {\mathrm{O}}_{\mathrm{2}}{(}^{\mathrm{3}}{\mathrm{\Sigma }}_g^{-})$ + O(³P) pathway, which is likely tolead to inaccuracies in aerosol measurements. Two recent studies haveinvestigated the use of O₃ for PAS calibration but have reachedseemingly contradictory conclusions with one finding that it results in asensitivity that is a factor of 2 low and the other concluding that it isaccurate. The present work is meant to add to this discussion by exploringthe extent to which O₃ photodissociates in the PAS cell and the rolethat the identity of the bath gas plays in determining the PAS sensitivity.We find a 5% loss in PAS signal attributable to photodissociation at 532nmin N₂ but no loss in a 5% mixture of O₂ in N₂.Furthermore, we discovered a dramatic increase of more than a factor of 2in the PAS sensitivity as we increased the O₂ fraction in the bathgas, which reached an asymptote near 100% O₂ that nearly matched thesensitivity measured with both NO₂ and nigrosin particles. Weinterpret this dependence with a kinetic model that suggests the reason forthe observed results is a more efficient transfer of energy from excitedO₃ to O₂ than to N₂ by a factor of 22–55 depending onexcitation wavelength. Notably, the two prior studies on this topic useddifferent bath gas compositions, and although the results presented here donot fully resolve the differences in their results, they may at leastpartially explain them.

    

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4. Mode of carbon and energy metabolism shifts lipid composition in the thermoacidophile Acidianus

   https://doi.org/10.1128/aem.01369-23  

   Rhim, Jeemin H. ; Zhou, Alice ; Amenabar, Maximiliano J. ; Boyer, Grayson M. ; Elling, Felix J. ; Weber, Yuki ; Pearson, Ann ; Boyd, Eric S. ; Leavitt, William D. ( January 2024 , Applied and Environmental Microbiology)

   Spear, John R. (Ed.)

   The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation to temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. The main objective of this study was to investigate the effect of carbon and energy metabolism on membrane cyclization. To do so, we cultivatedAcidianussp. DS80, a metabolically flexible and thermoacidophilic archaeon, on different electron donor, acceptor, and carbon source combinations (S⁰/Fe³⁺/CO₂, H₂/Fe³⁺/CO₂, H₂/S⁰/CO₂, or H₂/S⁰/glucose). We show that differences in energy and carbon metabolism can result in over a full unit of change in RI in the thermoacidophileAcidianussp. DS80. The patterns in RI correlated with the normalized electron transfer rate between the electron donor and acceptor and did not always align with thermodynamic predictions of energy yield. In light of this, we discuss other factors that may affect the kinetics of cellular energy metabolism: electron transfer chain (ETC) efficiency, location of ETC reaction components (cytoplasmicvs.extracellular), and the physical state of electron donors and acceptors (gasvs.solid). Furthermore, the assimilation of a more reduced form of carbon during heterotrophy appears to decrease the demand for reducing equivalents during lipid biosynthesis, resulting in lower RI. Together, these results point to the fundamental role of the cellular energy state in dictating GDGT cyclization, with those cells experiencing greater energy limitation synthesizing more cyclized GDGTs.

   Some archaea make unique membrane-spanning lipids with different numbers of five- or six-membered rings in the core structure, which modulate membrane fluidity and permeability. Changes in membrane core lipid composition reflect the fundamental adaptation strategies of archaea in response to stress, but multiple environmental and physiological factors may affect the needs for membrane fluidity and permeability. In this study, we tested howAcidianussp. DS80 changed its core lipid composition when grown with different electron donor/acceptor pairs. We show that changes in energy and carbon metabolisms significantly affected the relative abundance of rings in the core lipids of DS80. These observations highlight the need to better constrain metabolic parameters, in addition to environmental factors, which may influence changes in membrane physiology in Archaea. Such consideration would be particularly important for studying archaeal lipids from habitats that experience frequent environmental fluctuations and/or where metabolically diverse archaea thrive.

    

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5. Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni‐Mediated Oligomerization Shift

   https://doi.org/10.1002/chem.202202902  

   Prasad, Pallavi ; Hunt, Leigh Anna ; Pall, Ashley E. ; Ranasinghe, Maduni ; Williams, Ashley E. ; Stemmler, Timothy L. ; Demeler, Borries ; Hammer, Nathan I. ; Chakraborty, Saumen ( February 2023 , Chemistry – A European Journal)

   De novo metalloprotein design involves the construction of proteins guided by specific repeat patterns of polar and apolar residues, which, upon self‐assembly, provide a suitable environment to bind metals and produce artificial metalloenzymes. While a wide range of functionalities have been realized in de novo designed metalloproteins, the functional repertoire of such constructs towards alternative energy‐relevant catalysis is currently limited. Here we show the application of de novo approach to design a functional H₂evolving protein. The design involved the assembly of an amphiphilic peptide featuring cysteines at tandema/dsites of each helix. Intriguingly, upon Ni^IIaddition, the oligomers shift from a major trimeric assembly to a mix of dimers and trimers. The metalloprotein produced H₂photocatalytically with a bell‐shape pH dependence, having a maximum activity at pH 5.5. Transient absorption spectroscopy is used to determine the timescales of electron transfer as a function of pH. Selective outer sphere mutations are made to probe how the local environment tunes activity. A preferential enhancement of activity is observed via steric modulation above the Ni^IIsite, towards the N‐termini, compared to below the Ni^IIsite towards the C‐termini.

    

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