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1. An Extracellular, Ca ²⁺ ‐Activated Nuclease ( EcnA ) Mediates Transformation in a Naturally Competent Archaeon

   https://doi.org/10.1111/mmi.15311  

   Fonseca, Dallas R.; Day, Leslie A.; Crone, Kathryn K.; Costa, Kyle C. (August 2024, Molecular Microbiology)

   ABSTRACT Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation inMethanococcus maripaludis, but few homologs of bacterial transformation‐associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here asecnA), to be an extracellular nuclease. We show that EcnA is Ca²⁺‐activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation‐associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion. 

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2. Beyond bacterial paradigms: uncovering the functional significance and first biogenesis machinery of archaeal lipoproteins

   https://doi.org/10.1101/2024.08.27.609747  

   Hong, Yirui; Makarova, Kira S; Xu, Rachel; Pfeiffer, Friedhelm; Pohlschroder, Mechthild (August 2024, bioRxiv)

   Abstract Lipoproteins are major constituents of prokaryotic cell surfaces. In bacteria, lipoprotein attachment to membrane lipids is catalyzed by prolipoprotein diacylglyceryl transferase (Lgt). However, no Lgt homologs have been identified in archaea, suggesting the unique archaeal membrane lipids require distinct enzymes for lipoprotein lipidation. Here, we performedin silicopredictions for all major archaeal lineages and revealed a high prevalence of lipoproteins across the domain Archaea. Using comparative genomics, we identified the first set of candidates for archaeal lipoprotein biogenesis components (Ali). Genetic and biochemical characterization confirmed two paralogous genes,aliAandaliB, are important for lipoprotein lipidation in the archaeonHaloferax volcanii. Disruption of AliA- and AliB-mediated lipoprotein lipidation results in severe growth defects, decreased motility, and cell-shape alterations, underscoring the importance of lipoproteins in archaeal cell physiology. AliA and AliB also exhibit different enzymatic activities, including potential substrate selectivity, uncovering a new layer of regulation for prokaryotic lipoprotein lipidation. 

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3. The circadian clock and darkness control natural competence in cyanobacteria

   https://doi.org/10.1038/s41467-020-15384-9  

   Taton, Arnaud; Erikson, Christian; Yang, Yiling; Rubin, Benjamin E.; Rifkin, Scott A.; Golden, James W.; Golden, Susan S. (April 2020, Nature Communications)

   Abstract The cyanobacteriumSynechococcus elongatusis a model organism for the study of circadian rhythms. It is naturally competent for transformation—that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation inS. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length. 

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4. A large deletion at the cortex locus eliminates butterfly wing patterning

   https://doi.org/10.1093/g3journal/jkac021  

   Hanly, Joseph J.; Livraghi, Luca; Heryanto, Christa; McMillan, W. Owen; Jiggins, Chris D.; Gilbert, Lawrence E.; Martin, Arnaud; Oliver, ed., B. (January 2022, G3 Genes|Genomes|Genetics)

   Abstract As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations. 

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5. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma

   https://doi.org/10.1073/pnas.2310854121  

   Duan, Mingrui; Song, Shenghan; Wasserman, Hana; Lee, Po-Hsuen; Liu, Ke Jian; Gordân, Raluca; He, Yi; Mao, Peng (January 2024, Proceedings of the National Academy of Sciences)

   Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5′ side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genesRPL13AandRPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription. 

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