Structure of the transcription open complex of distinct σ
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
13 10 2023
13 10 2023
Historique:
received:
22
03
2023
accepted:
15
09
2023
medline:
23
10
2023
pubmed:
14
10
2023
entrez:
13
10
2023
Statut:
epublish
Résumé
Bacterial σ
Identifiants
pubmed: 37833284
doi: 10.1038/s41467-023-41796-4
pii: 10.1038/s41467-023-41796-4
pmc: PMC10575876
doi:
Substances chimiques
Bacterial Proteins
0
Sigma Factor
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6455Informations de copyright
© 2023. Springer Nature Limited.
Références
Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O. & Darst, S. A. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296, 1285–1290 (2002).
pubmed: 12016307
doi: 10.1126/science.1069595
Marr, M. T. & Roberts, J. W. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science 276, 1258–1260 (1997).
pubmed: 9157885
doi: 10.1126/science.276.5316.1258
Staroń, A. et al. The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family. Mol. Microbiol. 74, 557–581 (2009).
pubmed: 19737356
doi: 10.1111/j.1365-2958.2009.06870.x
Lonetto, M., Gribskov, M. & Gross, C. A. The σ
pubmed: 1597408
pmcid: 206090
doi: 10.1128/jb.174.12.3843-3849.1992
Paget, M. S. & Helmann, J. D. The σ
pubmed: 12540296
pmcid: 151288
doi: 10.1186/gb-2003-4-1-203
Pinto, D., Liu, Q. & Mascher, T. ECF σ factors with regulatory extensions: the one-component systems of the σ universe. Mol. Microbiol. 112, 399–409 (2019).
pubmed: 31175685
doi: 10.1111/mmi.14323
Brooks, B. E. & Buchanan, S. K. Signaling mechanisms for activation of extracytoplasmic function (ECF) sigma factors. Biochim. Biophys. Acta 1778, 1930–1945 (2008).
pubmed: 17673165
doi: 10.1016/j.bbamem.2007.06.005
Pinto, D. et al. Engineering orthogonal synthetic timer circuits based on extracytoplasmic function σ factors. Nucleic Acids Res. 46, 7450–7464 (2018).
pubmed: 29986061
pmcid: 6101570
doi: 10.1093/nar/gky614
Zuo, Y. & Steitz, T. A. Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol. Cell 58, 534–540 (2015).
pubmed: 25866247
pmcid: 5567806
doi: 10.1016/j.molcel.2015.03.010
Bae B., Feklistov A., Lass-Napiorkowska A., Landick R. & Darst S. A. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 4, e08504 (2015).
pubmed: 26349032
pmcid: 4593229
doi: 10.7554/eLife.08504
Cartagena, A. J. et al. Structural basis for transcription activation by Crl through tethering of σ
pubmed: 31484766
pmcid: 6754549
doi: 10.1073/pnas.1910827116
Liu, B., Zuo, Y. & Steitz, T. A. Structures of E. coli σ
pubmed: 27035955
pmcid: 4839411
doi: 10.1073/pnas.1520555113
Shi, W. et al. Structural basis of bacterial σ
pubmed: 32484956
pmcid: 7360974
doi: 10.15252/embj.2020104389
Lu, Q. et al. Structural insight into the mechanism of σ
pubmed: 37238608
pmcid: 10216364
doi: 10.3390/biom13050738
Fang, C. et al. Structures and mechanism of transcription initiation by bacterial ECF factors. Nucleic Acids Res. 47, 7094–7104 (2019).
pubmed: 31131408
pmcid: 6648896
doi: 10.1093/nar/gkz470
Li, L., Fang, C., Zhuang, N., Wang, T. & Zhang, Y. Structural basis for transcription initiation by bacterial ECF σ factors. Nat. Commun. 10, 1153 (2019).
pubmed: 30858373
pmcid: 6411747
doi: 10.1038/s41467-019-09096-y
Lin, W. et al. Structural basis of ECF-σ-factor-dependent transcription initiation. Nat. Commun. 10, 710 (2019).
pubmed: 30755604
pmcid: 6372665
doi: 10.1038/s41467-019-08443-3
Glyde, R. et al. Structures of RNA polymerase closed and intermediate complexes reveal mechanisms of DNA opening and transcription initiation. Mol. Cell 67, 106–116 (2017).
pubmed: 28579332
pmcid: 5505868
doi: 10.1016/j.molcel.2017.05.010
Campbell, E. A., Kamath, S., Rajashankar, K. R., Wu, M. & Darst, S. A. Crystal structure of Aquifex aeolicus σ
pubmed: 28223493
pmcid: 5347599
doi: 10.1073/pnas.1619464114
Nataf, Y. et al. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc. Natl Acad. Sci. USA 107, 18646–18651 (2010).
pubmed: 20937888
pmcid: 2972930
doi: 10.1073/pnas.1012175107
Ramaniuk, O. et al. σ
pubmed: 29914988
pmcid: 6088155
doi: 10.1128/JB.00251-18
Zuber, U., Drzewiecki, K. & Hecker, M. Putative sigma factor SigI (YkoZ) of Bacillus subtilis is induced by heat shock. J. Bacteriol. 183, 1472–1475 (2001).
pubmed: 11157964
pmcid: 95025
doi: 10.1128/JB.183.4.1472-1475.2001
Wei, Z. et al. Alternative σ
pubmed: 31106374
pmcid: 6582324
doi: 10.1093/nar/gkz355
Kahel-Raifer, H. et al. The unique set of putative membrane-associated anti-σ factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation. FEMS Microbiol. Lett. 308, 84–93 (2010).
pubmed: 20487018
doi: 10.1111/j.1574-6968.2010.01997.x
Casas-Pastor, D. et al. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 49, 986–1005 (2021).
pubmed: 33398323
pmcid: 7826278
doi: 10.1093/nar/gkaa1229
Gruber, T. M. & Gross, C. A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57, 441–466 (2003).
pubmed: 14527287
doi: 10.1146/annurev.micro.57.030502.090913
Ortiz de Ora, L. et al. Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia. Sci. Rep. 8, 11036 (2018).
pubmed: 30038431
pmcid: 6056542
doi: 10.1038/s41598-018-29245-5
Muñoz-Gutiérrez, I. et al. Decoding biomass-sensing regulons of Clostridium thermocellum alternative sigma-I factors in a heterologous Bacillus subtilis host system. PLoS ONE 11, e0146316 (2016).
pubmed: 26731480
pmcid: 4711584
doi: 10.1371/journal.pone.0146316
Izquierdo, J. A. et al. Complete genome sequence of Clostridium clariflavum DSM 19732. Stand. Genom. Sci. 6, 104–115 (2012).
doi: 10.4056/sigs.2535732
Yaniv, O. et al. Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σ
doi: 10.1107/S139900471302926X
Ding, X. K., Chen, C., Cui, Q., Li, W. L. & Feng, Y. G. Resonance assignments of the periplasmic domain of a cellulose-sensing trans-membrane anti-sigma factor from Clostridium thermocellum. Biomol. NMR Assign. 9, 321–324 (2015).
pubmed: 25682099
doi: 10.1007/s12104-015-9601-7
Chen, C. et al. Essential autoproteolysis of bacterial anti-σ factor RsgI for transmembrane signal transduction. Sci. Adv. 9, eadg4846 (2023).
pubmed: 37418529
pmcid: 10328401
doi: 10.1126/sciadv.adg4846
Brunet, Y. R., Habib, C., Brogan, A. P., Artzi, L. & Rudner, D. Z. Intrinsically disordered protein regions are required for cell wall homeostasis in Bacillus subtilis. Genes Dev. 36, 970–984 (2022).
pubmed: 36265902
pmcid: 9732909
Narayanan, A. et al. Cryo-EM structure of Escherichia coli σ
pubmed: 29581236
pmcid: 5949986
doi: 10.1074/jbc.RA118.002161
Shi, J. et al. Transcription activation by a sliding clamp. Nat. Commun. 12, 1131 (2021).
pubmed: 33602900
pmcid: 7892883
doi: 10.1038/s41467-021-21392-0
Boyaci, H., Chen, J., Jansen, R., Darst, S. A. & Campbell, E. A. Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature 565, 382–385 (2019).
pubmed: 30626968
pmcid: 6399747
doi: 10.1038/s41586-018-0840-5
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Zhang, X. et al. Molecular basis of TcdR-dependent promoter activity for toxin production by Clostridioides difficile studied by a heterologous reporter system. Toxins 15, 306 (2023).
pubmed: 37235341
pmcid: 10223161
doi: 10.3390/toxins15050306
Fang, C. et al. CueR activates transcription through a DNA distortion mechanism. Nat. Chem. Biol. 17, 57–64 (2021).
pubmed: 32989300
doi: 10.1038/s41589-020-00653-x
Burkhoff, A. M. & Tullius, T. D. The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell 48, 935–943 (1987).
pubmed: 3030560
doi: 10.1016/0092-8674(87)90702-1
Neidle S. In Principles of Nucleic Acid Structure (ed. Neidle S.). (Academic Press, 2008).
Barbic, A., Zimmer, D. P. & Crothers, D. M. Structural origins of adenine-tract bending. Proc. Natl. Acad. Sci. USA 100, 2369–2373 (2003).
pubmed: 12586860
pmcid: 151347
doi: 10.1073/pnas.0437877100
Fang, C. et al. The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription. Nat. Commun. 11, 6284 (2020).
pubmed: 33293519
pmcid: 7722741
doi: 10.1038/s41467-020-20134-y
Lane, W. J. & Darst, S. A. The structural basis for promoter −35 element recognition by the group IV sigma factors. PLoS Biol. 4, e269 (2006).
pubmed: 16903784
pmcid: 1540707
doi: 10.1371/journal.pbio.0040269
Holm, L. & Rosenström, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, 275–288 (2010).
doi: 10.1093/nar/gkq366
Light, S. H., Cahoon, L. A., Halavaty, A. S., Freitag, N. E. & Anderson, W. F. Structure to function of an α-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Nat. Microbiol. 2, 16202 (2016).
pubmed: 27819654
doi: 10.1038/nmicrobiol.2016.202
Chen, J. et al. Stepwise promoter melting by bacterial RNA polymerase. Mol. Cell 78, 275–288 (2020).
pubmed: 32160514
pmcid: 7166197
doi: 10.1016/j.molcel.2020.02.017
Saecker, R. M. et al. Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc. Natl. Acad. Sci. USA 118, e2112877118 (2021).
pubmed: 34599106
pmcid: 8501879
doi: 10.1073/pnas.2112877118
Wang, F. et al. Structural basis for transcription inhibition by E. coli SspA. Nucleic Acids Res. 48, 9931–9942 (2020).
pubmed: 32785630
pmcid: 7515715
doi: 10.1093/nar/gkaa672
Campagne, S., Marsh, M. E., Capitani, G., Vorholt, J. A. & Allain, F. H. T. Structural basis for −10 promoter element melting by environmentally induced sigma factors. Nat. Struct. Mol. Biol. 21, 269–276 (2014).
pubmed: 24531660
doi: 10.1038/nsmb.2777
Pinto, D. & da Fonseca, R. R. Evolution of the extracytoplasmic function σ factor protein family. NAR Genom. Bioinform. 2, lqz026 (2020).
pubmed: 33575573
pmcid: 7671368
doi: 10.1093/nargab/lqz026
Crane-Robinson, C., Dragan, A. I. & Privalov, P. L. The extended arms of DNA-binding domains: a tale of tails. Trends Biochem. Sci. 31, 547–552 (2006).
pubmed: 16920361
doi: 10.1016/j.tibs.2006.08.006
Rohs, R. et al. The role of DNA shape in protein–DNA recognition. Nature 461, 1248–1253 (2009).
pubmed: 19865164
pmcid: 2793086
doi: 10.1038/nature08473
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).
pubmed: 15808743
doi: 10.1016/j.femsre.2004.12.008
Bayer, E. A., Morag, E. & Lamed, R. The cellulosome—a treasure-trove for biotechnology. Trends Biotechnol. 12, 379–386 (1994).
pubmed: 7765191
doi: 10.1016/0167-7799(94)90039-6
Feng, Y., Liu, Y.-J. & Cui, Q. Research progress in cellulosomes and their applications in synthetic biology. Synth. Biol. J. 3, 138–154 (2022).
Ma, X., Ma, L. & Huo, Y. X. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol. 40, 735–751 (2022).
pubmed: 34895933
doi: 10.1016/j.tibtech.2021.11.002
Zong, Y. et al. Insulated transcriptional elements enable precise design of genetic circuits. Nat. Commun. 8, 52 (2017).
pubmed: 28674389
pmcid: 5495784
doi: 10.1038/s41467-017-00063-z
Zhang, J. et al. Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum. Biotechnol. Biofuels 10, 124 (2017).
Qi, K. et al. Coordinated β-glucosidase activity with the cellulosome is effective for enhanced lignocellulose saccharification. Bioresour. Technol. 337, 125441 (2021).
pubmed: 34182347
doi: 10.1016/j.biortech.2021.125441
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
pubmed: 16182563
doi: 10.1016/j.jsb.2005.07.007
Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019).
pubmed: 31591575
pmcid: 6858868
doi: 10.1038/s41592-019-0580-y
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021).
pubmed: 33542510
pmcid: 8183613
doi: 10.1038/s41592-020-01049-4
Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. V. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923–927 (2020).
pubmed: 32807957
pmcid: 7484085
doi: 10.1038/s41592-020-0914-9
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
pubmed: 34267316
pmcid: 8282847
doi: 10.1038/s42003-021-02399-1
Pettersen, E. F. et al. UCSF Chimera—visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254
doi: 10.1002/jcc.20084
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. Sect. D. Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
pubmed: 28710774
doi: 10.1002/pro.3235
Härtl, B., Wehrl, W., Wiegert, T., Homuth, G. & Schumann, W. Development of a new integration site within the Bacillus subtilis chromosome and construction of compatible expression cassettes. J. Bacteriol. 183, 2696–2699 (2001).
pubmed: 11274134
pmcid: 95191
doi: 10.1128/JB.183.8.2696-2699.2001
Guiziou, S. et al. A part toolbox to tune genetic expression in Bacillus subtilis. Nucleic Acids Res. 44, 7495–7508 (2016).
pubmed: 27402159
pmcid: 5009755
Radeck, J. et al. The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J. Biol. Eng. 7, 29 (2013).
pubmed: 24295448
pmcid: 4177231
doi: 10.1186/1754-1611-7-29
Trachman, R. J. 3rd et al. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat. Chem. Biol. 13, 807–813 (2017).
pubmed: 28553947
pmcid: 5550021
doi: 10.1038/nchembio.2392
He, D. et al. Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. Nat. Commun. 13, 4204 (2022).
pubmed: 35859063
pmcid: 9300723
doi: 10.1038/s41467-022-31871-7