Aravind, L., Anantharaman, V., Balaji, S., Babu, M. M. & Iyer, L. M. The many faces of the helix–turn–helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29, 231–262 (2005).
Birkholz, N., Fagerlund, R. D., Smith, L. M., Jackson, S. A. & Fineran, P. C. The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Res. 47, 9658–9665 (2019).
Stanley, S. Y. et al. Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription. Cell 178, 1452–1464 (2019).
Shehreen, S., Birkholz, N., Fineran, Peter, C. & Brown, C. M. Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Res. 50, 8615–8625 (2022).
Lee, S. Y., Birkholz, N., Fineran, P. C. & Park, H. H. Molecular basis of anti-CRISPR operon repression by Aca10. Nucleic Acids Res. 50, 8919–8928 (2022).
Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961).
Laughon, A. & Scott, M. P. Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins. Nature 310, 25–31 (1984).
McGinnis, W., Garber, R. L., Wirz, J., Kuroiwa, A. & Gehring, W. J. A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37, 403–408 (1984).
Bürglin, T. R. & Affolter, M. Homeodomain proteins: an update. Chromosoma 125, 497–521 (2016).
Biedenkapp, H., Borgmeyer, U., Sippel, A. E. & Klempnauer, K.-H. Viral myb oncogene encodes a sequence-specific DNA-binding activity. Nature 335, 835–837 (1988).
McKay, D. B. & Steitz, T. A. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744–749 (1981).
Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature 290, 754–758 (1981).
Mayo-Muñoz, D., Pinilla-Redondo, R., Birkholz, N. & Fineran, P. C. A host of armor: prokaryotic immune strategies against mobile genetic elements. Cell Rep. 42, 112672 (2023).
Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429–432 (2013).
Pawluk, A. et al. Inactivation of CRISPR–Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat. Microbiol. 1, 16085 (2016).
Usher, B. et al. Crystal structure of the anti-CRISPR repressor Aca2. J. Struct. Biol. 213, 107752 (2021).
Lee, S. Y., Kim, G. E. & Park, H. H. Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2. Acta Crystallogr. D 78, 59–68 (2022).
Liu, Y. et al. Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2. J. Biol. Chem. 297, 101357 (2021).
Meaden, S. et al. Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity. ISME J. 15, 534–544 (2021).
Tovkach, F. I. Study of Erwinia carotovora phage resistance with the use of temperate bacteriophage ZF40. Microbiology 71, 72–77 (2002).
Zhang, K. et al. Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR–Cas complex revealed by cryo-EM. Proc. Natl Acad. Sci. USA 117, 7176–7182 (2020).
Chen, Y.-J. et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods 10, 659–664 (2013).
Osuna, B. A. et al. Critical Anti-CRISPR locus repression by a bi-functional Cas9 inhibitor. Cell Host Microbe 28, 23–30 (2020).
Kimanius, D. et al. Data-driven regularisation lowers the size barrier of cryo-EM structure determination. Nat. Methods https://doi.org/10.1038/s41592-024-02304-8 (2024).
Segall-Shapiro, T. H., Sontag, E. D. & Voigt, C. A. Engineered promoters enable constant gene expression at any copy number in bacteria. Nat. Biotechnol. 36, 352–358 (2018).
Bleris, L. et al. Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Mol. Syst. Biol. 7, 519 (2011).
Rivera-Pomar, R., Niessing, D., Schmidt-Ott, U., Gehring, W. J. & Jacklë, H. RNA binding and translational suppression by bicoid. Nature 379, 746–749 (1996).
Alfano, C. et al. Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat. Struct. Mol. Biol. 11, 323–329 (2004).
Dong, G., Chakshusmathi, G., Wolin, S. L. & Reinisch, K. M. Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch. EMBO J. 23, 1000–1007 (2004).
Tan, D., Zhou, M., Kiledjian, M. & Tong, L. The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA. Nat. Struct. Mol. Biol. 21, 679–685 (2014).
Schlundt, A. et al. Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation. Nat. Struct. Mol. Biol. 21, 671–678 (2014).
Soler, N., Fourmy, D. & Yoshizawa, S. Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. J. Mol. Biol. 370, 728–741 (2007).
Yoshizawa, S. et al. Structural basis for mRNA recognition by elongation factor SelB. Nat. Struct. Mol. Biol. 12, 198–203 (2005).
Morrison, J., Anderson, K., Beenken, K., Smeltzer, M. & Dunman, P. The staphylococcal accessory regulator, SarA, is an RNA-binding protein that modulates the mRNA turnover properties of late-exponential and stationary phase Staphylococcus aureus cells. Front. Cell. Infect. Microbiol. 2, 26 (2012).
Chu, L.-C. et al. The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix–turn–helix DNA-binding and Rossmann-fold proteins. Nat. Commun. 13, 2883 (2022).
Conrad, T. et al. Serial interactome capture of the human cell nucleus. Nat. Commun. 7, 11212 (2016).
Oksuz, O. et al. Transcription factors interact with RNA to regulate genes. Mol. Cell 83, 2449–2463.e2413 (2023).
Madeira, F. et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47, W636–W641 (2019).
LaFleur, T. L., Hossain, A. & Salis, H. M. Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nat. Commun. 13, 5159 (2022).
Solovyev, V. & Salamov, A. in Metagenomics and its applications in agriculture, biomedicine and environmental studies (ed. Li, R. W.) 61–78 (Nova Science Publishers, 2011).
Proctor, J. R. & Meyer, I. M. CoFold: An RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Res. 41, e102 (2013).
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R. & Hofacker, I. L. The Vienna RNA Websuite. Nucleic Acids Res. 36, W70–W74 (2008).
Cai, Y. et al. A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. Sci. Adv. 6, eabb6651 (2020).
Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J 478, 4169–4185 (2021).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
Casañal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1055–1064 (2020).
Croll, T. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
Kubitschek, H. E. & Friske, J. A. Determination of bacterial cell volume with the Coulter counter. J. Bacteriol. 168, 1466–1467 (1986).
Gillespie, D. T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Will, S., Reiche, K., Hofacker, I. L., Stadler, P. F. & Backofen, R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol. 3, e65 (2007).
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).
Yao, Z., Weinberg, Z. & Ruzzo, W. L. CMfinder—a covariance model based RNA motif finding algorithm. Bioinformatics 22, 445–452 (2005).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Nordberg, H. et al. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 42, D26–D31 (2014).
Di Tommaso, P. et al. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39, W13–W17 (2011).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
A federal jury in Delaware determined on Friday that Qualcomm didn’t breach its agreement with…
Geese The Wendy Award The Apprentice What have you read/watched/listened to lately? Phoebe Ward, 22,…
15% ROI, 5% down loans!","body":"3.99% rate, 5% down! Access the BEST deals in the US…
Particles in ship exhaust inadvertently cause cloud brightening – some geoengineering projects would try to…
The weather outside is frightful, but the iOS games are so delightful, let it play,…
A few flagship bond funds from some big-name Southern California-based firms saw outflows of more…