Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host.
Mycobacterium tuberculosis
/ genetics
Rec A Recombinases
/ metabolism
Inteins
/ genetics
Bacterial Proteins
/ genetics
Protein Splicing
Escherichia coli
/ genetics
Exteins
/ genetics
DNA Damage
Proteasome Endopeptidase Complex
/ metabolism
Gene Expression Regulation, Bacterial
Promoter Regions, Genetic
Serine Endopeptidases
DNA damage repair
Exaptation
Gene expression
Mobile elements
Post-translational gene regulation
SOS response
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 Sep 2024
05 Sep 2024
Historique:
received:
17
04
2024
accepted:
26
08
2024
medline:
6
9
2024
pubmed:
6
9
2024
entrez:
5
9
2024
Statut:
epublish
Résumé
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
Identifiants
pubmed: 39237639
doi: 10.1038/s41598-024-71248-y
pii: 10.1038/s41598-024-71248-y
doi:
Substances chimiques
Rec A Recombinases
EC 2.7.7.-
Bacterial Proteins
0
LexA protein, Bacteria
0
Proteasome Endopeptidase Complex
EC 3.4.25.1
Serine Endopeptidases
EC 3.4.21.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
20664Informations de copyright
© 2024. The Author(s).
Références
Martin, C. J., Carey, A. F. & Fortune, S. M. A bug’s life in the granuloma. Semin. Immunopathol. 38, 213–220. https://doi.org/10.1007/s00281-015-0533-1 (2016).
doi: 10.1007/s00281-015-0533-1
pubmed: 26577238
Singh, A. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis. Microbiology (Reading) 163, 1740–1758. https://doi.org/10.1099/mic.0.000578 (2017).
doi: 10.1099/mic.0.000578
pubmed: 29171825
Boshoff, H. I., Reed, M. B., Barry, C. E. 3rd. & Mizrahi, V. DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 113, 183–193. https://doi.org/10.1016/s0092-8674(03)00270-8 (2003).
doi: 10.1016/s0092-8674(03)00270-8
pubmed: 12705867
Stephanou, N. C. et al. Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks. J. Bacteriol. 189, 5237–5246. https://doi.org/10.1128/JB.00332-07 (2007).
doi: 10.1128/JB.00332-07
pubmed: 17496093
pmcid: 1951864
Sander, P. et al. Mycobacterium bovis BCG recA deletion mutant shows increased susceptibility to DNA-damaging agents but wild-type survival in a mouse infection model. Infect. Immun. 69, 3562–3568. https://doi.org/10.1128/IAI.69.6.3562-3568.2001 (2001).
doi: 10.1128/IAI.69.6.3562-3568.2001
pubmed: 11349014
pmcid: 98336
Sassetti, C. M. & Rubin, E. J. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. U. S. A. 100, 12989–12994. https://doi.org/10.1073/pnas.2134250100 (2003).
doi: 10.1073/pnas.2134250100
pubmed: 14569030
pmcid: 240732
Wipperman, M. F. et al. Mycobacterial mutagenesis and drug resistance are controlled by phosphorylation- and cardiolipin-mediated inhibition of the RecA coprotease. Mol. Cell 72, 152-161 e157. https://doi.org/10.1016/j.molcel.2018.07.037 (2018).
doi: 10.1016/j.molcel.2018.07.037
pubmed: 30174294
pmcid: 6389330
Gopaul, K. K., Brooks, P. C., Prost, J. F. & Davis, E. O. Characterization of the two Mycobacterium tuberculosis recA promoters. J. Bacteriol. 185, 6005–6015 (2003).
doi: 10.1128/JB.185.20.6005-6015.2003
pubmed: 14526011
pmcid: 225015
Prasad, D. & Muniyappa, K. The anionic phospholipids in the plasma membrane play an important role in regulating the biochemical properties and biological functions of RecA proteins. Biochemistry 58, 1295–1310. https://doi.org/10.1021/acs.biochem.8b01147 (2019).
doi: 10.1021/acs.biochem.8b01147
pubmed: 30726069
Novikova, O., Topilina, N. & Belfort, M. Enigmatic distribution, evolution, and function of inteins. J. Biol. Chem. 289, 14490–14497. https://doi.org/10.1074/jbc.R114.548255 (2014).
doi: 10.1074/jbc.R114.548255
pubmed: 24695741
pmcid: 4031506
Mills, K. V., Johnson, M. A. & Perler, F. B. Protein splicing: how inteins escape from precursor proteins. J. Biol. Chem. 289, 14498–14505. https://doi.org/10.1074/jbc.R113.540310 (2014).
doi: 10.1074/jbc.R113.540310
pubmed: 24695729
pmcid: 4031507
Zhang, L., Zheng, Y., Callahan, B., Belfort, M. & Liu, Y. Cisplatin inhibits protein splicing, suggesting inteins as therapeutic targets in mycobacteria. J. Biol. Chem. 286, 1277–1282. https://doi.org/10.1074/jbc.M110.171124 (2011).
doi: 10.1074/jbc.M110.171124
pubmed: 21059649
Liu, X. Q. & Yang, J. Prp8 intein in fungal pathogens: target for potential antifungal drugs. FEBS Lett. 572, 46–50. https://doi.org/10.1016/j.febslet.2004.07.016 (2004).
doi: 10.1016/j.febslet.2004.07.016
pubmed: 15304322
Cheriyan, M. & Perler, F. B. Protein splicing: A versatile tool for drug discovery. Adv. Drug Deliv. Rev. 61, 899–907. https://doi.org/10.1016/j.addr.2009.04.021 (2009).
doi: 10.1016/j.addr.2009.04.021
pubmed: 19442693
Saves, I., Westrelin, F., Daffe, M. & Masson, J. M. Identification of the first eubacterial endonuclease coded by an intein allele in the pps1 gene of mycobacteria. Nucleic Acids Res. 29, 4310–4318 (2001).
doi: 10.1093/nar/29.21.4310
pubmed: 11691918
pmcid: 60189
Davis, E. O., Sedgwick, S. G. & Colston, M. J. Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product. J. Bacteriol. 173, 5653–5662 (1991).
doi: 10.1128/jb.173.18.5653-5662.1991
pubmed: 1909321
pmcid: 208294
Pietrokovski, S. Intein spread and extinction in evolution. Trends Genet. 17, 465–472 (2001).
doi: 10.1016/S0168-9525(01)02365-4
pubmed: 11485819
Nicastri, M. C. et al. Internal disulfide bond acts as a switch for intein activity. Biochemistry 52, 5920–5927. https://doi.org/10.1021/bi400736c (2013).
doi: 10.1021/bi400736c
pubmed: 23906287
Topilina, N. I. et al. SufB intein of Mycobacterium tuberculosis as a sensor for oxidative and nitrosative stresses. Proc. Natl. Acad. Sci. U. S. A. 112, 10348–10353. https://doi.org/10.1073/pnas.1512777112 (2015).
doi: 10.1073/pnas.1512777112
pubmed: 26240361
pmcid: 4547236
Topilina, N. I., Novikova, O., Stanger, M., Banavali, N. K. & Belfort, M. Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing. Nucleic Acids Res. 43, 6631–6648. https://doi.org/10.1093/nar/gkv612 (2015).
doi: 10.1093/nar/gkv612
pubmed: 26101259
pmcid: 4513877
Chong, S., Williams, K. S., Wotkowicz, C. & Xu, M. Q. Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. J. Biol. Chem. 273, 10567–10577 (1998).
doi: 10.1074/jbc.273.17.10567
pubmed: 9553117
Lennon, C. W., Stanger, M., Banavali, N. K. & Belfort, M. Conditional protein splicing switch in hyperthermophiles through an intein-extein partnership. mBio https://doi.org/10.1128/mBio.02304-17 (2018).
doi: 10.1128/mBio.02304-17
pubmed: 29921664
pmcid: 6016248
Lennon, C. W., Stanger, M. & Belfort, M. Protein splicing of a recombinase intein induced by ssDNA and DNA damage. Genes Dev. 30, 2663–2668. https://doi.org/10.1101/gad.289280.116 (2016).
doi: 10.1101/gad.289280.116
pubmed: 28031248
pmcid: 5238726
Lennon, C. W., Stanger, M. J. & Belfort, M. Mechanism of single-stranded DNA activation of recombinase intein splicing. Biochemistry 58, 3335–3339. https://doi.org/10.1021/acs.biochem.9b00506 (2019).
doi: 10.1021/acs.biochem.9b00506
pubmed: 31318538
Davis, E. O., Jenner, P. J., Brooks, P. C., Colston, M. J. & Sedgwick, S. G. Protein splicing in the maturation of M. tuberculosis RecA protein: A mechanism for tolerating a novel class of intervening sequence. Cell 71, 201–210 (1992).
doi: 10.1016/0092-8674(92)90349-H
pubmed: 1423588
Martin, D. D., Xu, M. Q. & Evans, T. C. Jr. Characterization of a naturally occurring trans-splicing intein from Synechocystis sp. PCC6803. Biochemistry 40, 1393–1402 (2001).
doi: 10.1021/bi001786g
pubmed: 11170467
Lennon, C. W., Wahl, D., Goetz, J. R. & Weinberger, J. Reactive chlorine species reversibly inhibit DnaB protein splicing in mycobacteria. Microbiol. Spectr. 9, e0030121. https://doi.org/10.1128/Spectrum.00301-21 (2021).
doi: 10.1128/Spectrum.00301-21
pubmed: 34549994
Woods, D. et al. Conditional DnaB protein splicing is reversibly inhibited by zinc in mycobacteria. mBio https://doi.org/10.1128/mBio.01403-20 (2020).
doi: 10.1128/mBio.01403-20
pubmed: 32665276
pmcid: 7360933
Kelley, D. S. et al. Mycobacterial DnaB helicase intein as oxidative stress sensor. Nat. Commun. 9, 4363. https://doi.org/10.1038/s41467-018-06554-x (2018).
doi: 10.1038/s41467-018-06554-x
pubmed: 30341292
pmcid: 6195587
Zhang, L. et al. Binding and inhibition of copper ions to RecA inteins from Mycobacterium tuberculosis. Chemistry 16, 4297–4306. https://doi.org/10.1002/chem.200903584 (2010).
doi: 10.1002/chem.200903584
pubmed: 20209535
Davis, E. O., Dullaghan, E. M. & Rand, L. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J. Bacteriol. 184, 3287–3295. https://doi.org/10.1128/JB.184.12.3287-3295.2002 (2002).
doi: 10.1128/JB.184.12.3287-3295.2002
pubmed: 12029045
pmcid: 135081
Davis, E. O. et al. DNA damage induction of recA in Mycobacterium tuberculosis independently of RecA and LexA. Mol. Microbiol. 46, 791–800. https://doi.org/10.1046/j.1365-2958.2002.03199.x (2002).
doi: 10.1046/j.1365-2958.2002.03199.x
pubmed: 12410836
Papavinasasundaram, K. G. et al. Slow induction of RecA by DNA damage in Mycobacterium tuberculosis. Microbiology (Reading) 147, 3271–3279. https://doi.org/10.1099/00221287-147-12-3271 (2001).
doi: 10.1099/00221287-147-12-3271
pubmed: 11739759
Movahedzadeh, F., Colston, M. J. & Davis, E. O. Determination of DNA sequences required for regulated Mycobacterium tuberculosis RecA expression in response to DNA-damaging agents suggests that two modes of regulation exist. J. Bacteriol. 179, 3509–3518 (1997).
doi: 10.1128/jb.179.11.3509-3518.1997
pubmed: 9171394
pmcid: 179142
Ward, S. K., Hoye, E. A. & Talaat, A. M. The global responses of Mycobacterium tuberculosis to physiological levels of copper. J. Bacteriol. 190, 2939–2946. https://doi.org/10.1128/JB.01847-07 (2008).
doi: 10.1128/JB.01847-07
pubmed: 18263720
pmcid: 2293257
Rowland, J. L. & Niederweis, M. A multicopper oxidase is required for copper resistance in Mycobacterium tuberculosis. J. Bacteriol. 195, 3724–3733. https://doi.org/10.1128/JB.00546-13 (2013).
doi: 10.1128/JB.00546-13
pubmed: 23772064
pmcid: 3754562
Bal, W., Sokolowska, M., Kurowska, E. & Faller, P. Binding of transition metal ions to albumin: Sites, affinities and rates. Biochim. Biophys. Acta 1830, 5444–5455. https://doi.org/10.1016/j.bbagen.2013.06.018 (2013).
doi: 10.1016/j.bbagen.2013.06.018
pubmed: 23811338
Eastman, A. Characterization of the adducts produced in DNA by cis-diamminedichloroplatinum(II) and cis-dichloro(ethylenediamine)platinum(II). Biochemistry 22, 3927–3933 (1983).
doi: 10.1021/bi00285a031
pubmed: 6225458
Bruhn, S. L., Toney, J. H. & Lippard, S. J. Biological processing of DNA modified by platinum compounds. Prog. Inorg. Chem. 38, 477–516. https://doi.org/10.1002/9780470166390.ch8 (1990).
doi: 10.1002/9780470166390.ch8
Darwin, K. H., Ehrt, S., Gutierrez-Ramos, J. C., Weich, N. & Nathan, C. F. The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide. Science 302, 1963–1966. https://doi.org/10.1126/science.1091176 (2003).
doi: 10.1126/science.1091176
pubmed: 14671303
Festa, R. A. et al. Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected]. PLoS One 5, e8589. https://doi.org/10.1371/journal.pone.0008589 (2010).
doi: 10.1371/journal.pone.0008589
pubmed: 20066036
pmcid: 2797603
Hu, G. et al. Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate. Mol. Microbiol. 59, 1417–1428. https://doi.org/10.1111/j.1365-2958.2005.05036.x (2006).
doi: 10.1111/j.1365-2958.2005.05036.x
pubmed: 16468986
Muller, A. U., Imkamp, F. & Weber-Ban, E. The mycobacterial LexA/RecA-independent DNA damage response is controlled by PafBC and the Pup-proteasome system. Cell Rep. 23, 3551–3564. https://doi.org/10.1016/j.celrep.2018.05.073 (2018).
doi: 10.1016/j.celrep.2018.05.073
pubmed: 29924998
Horii, T., Ozawa, N., Ogawa, T. & Ogawa, H. Inhibitory effects of N- and C-terminal truncated Escherichia coli recA gene products on functions of the wild-type recA gene. J. Mol. Biol. 223, 105–114. https://doi.org/10.1016/0022-2836(92)90719-z (1992).
doi: 10.1016/0022-2836(92)90719-z
pubmed: 1731063
Karlin, S. & Brocchieri, L. Evolutionary conservation of RecA genes in relation to protein structure and function. J. Bacteriol. 178, 1881–1894. https://doi.org/10.1128/jb.178.7.1881-1894.1996 (1996).
doi: 10.1128/jb.178.7.1881-1894.1996
pubmed: 8606161
pmcid: 177882
Nair, S. & Steyn, L. M. Cloning and expression in Escherichia coli of a recA homologue from Mycobacterium tuberculosis. J. Gen. Microbiol. 137, 2409–2414. https://doi.org/10.1099/00221287-137-10-2409 (1991).
doi: 10.1099/00221287-137-10-2409
pubmed: 1770355
Wade, J. T., Reppas, N. B., Church, G. M. & Struhl, K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19, 2619–2630. https://doi.org/10.1101/gad.1355605 (2005).
doi: 10.1101/gad.1355605
pubmed: 16264194
pmcid: 1276735
Walker, G. C. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 48, 60–93. https://doi.org/10.1128/mr.48.1.60-93.1984 (1984).
doi: 10.1128/mr.48.1.60-93.1984
pubmed: 6371470
pmcid: 373003
Guhan, N. & Muniyappa, K. Mycobacterium tuberculosis RecA intein possesses a novel ATP-dependent site-specific double-stranded DNA endonuclease activity. J. Biol. Chem. 277, 16257–16264. https://doi.org/10.1074/jbc.M112365200 (2002).
doi: 10.1074/jbc.M112365200
pubmed: 11850426
Guhan, N. & Muniyappa, K. The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations. J. Biol. Chem. 277, 40352–40361. https://doi.org/10.1074/jbc.M205697200 (2002).
doi: 10.1074/jbc.M205697200
pubmed: 12167644
Guhan, N. & Muniyappa, K. Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn(2+) and DNA-dependent ATPase activity. Nucleic Acids Res. 31, 4184–4191. https://doi.org/10.1093/nar/gkg475 (2003).
doi: 10.1093/nar/gkg475
pubmed: 12853636
pmcid: 167636
Wood, D. W., Belfort, M. & Lennon, C. W. Inteins-mechanism of protein splicing, emerging regulatory roles, and applications in protein engineering. Front. Microbiol. 14, 1305848. https://doi.org/10.3389/fmicb.2023.1305848 (2023).
doi: 10.3389/fmicb.2023.1305848
pubmed: 38029209
pmcid: 10663303
Hill, P. W. S. et al. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 29, 1757-1773 e1710. https://doi.org/10.1016/j.chom.2021.10.002 (2021).
doi: 10.1016/j.chom.2021.10.002
pubmed: 34731646
Salini, S. et al. The error-prone polymerase DnaE2 mediates the evolution of antibiotic resistance in persister mycobacterial cells. Antimicrob. Agents Chemother. 66, e0177321. https://doi.org/10.1128/AAC.01773-21 (2022).
doi: 10.1128/AAC.01773-21
pubmed: 35156855
Tomasz, M. Mitomycin C: Small, fast and deadly (but very selective). Chem. Biol. 2, 575–579. https://doi.org/10.1016/1074-5521(95)90120-5 (1995).
doi: 10.1016/1074-5521(95)90120-5
pubmed: 9383461
Drlica, K. & Zhao, X. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol. Mol. Biol. Rev. 61, 377–392. https://doi.org/10.1128/mmbr.61.3.377-392.1997 (1997).
doi: 10.1128/mmbr.61.3.377-392.1997
pubmed: 9293187
pmcid: 232616
Cumming, B. M. et al. The physiology and genetics of oxidative stress in mycobacteria. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.MGM2-0019-2013 (2014).
doi: 10.1128/microbiolspec.MGM2-0019-2013
pubmed: 26103972
Ehrt, S. & Schnappinger, D. Mycobacterial survival strategies in the phagosome: Defence against host stresses. Cell Microbiol. 11, 1170–1178. https://doi.org/10.1111/j.1462-5822.2009.01335.x (2009).
doi: 10.1111/j.1462-5822.2009.01335.x
pubmed: 19438516
pmcid: 3170014
Newton, G. L., Buchmeier, N. & Fahey, R. C. Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria. Microbiol. Mol. Biol. Rev. 72, 471–494. https://doi.org/10.1128/MMBR.00008-08 (2008).
doi: 10.1128/MMBR.00008-08
pubmed: 18772286
pmcid: 2546866
Stafford, S. L. et al. Metal ions in macrophage antimicrobial pathways: Emerging roles for zinc and copper. Biosci. Rep. https://doi.org/10.1042/BSR20130014 (2013).
Lee, A. K., Detweiler, C. S. & Falkow, S. OmpR regulates the two-component system SsrA-ssrB in Salmonella pathogenicity island 2. J. Bacteriol. 182, 771–781 (2000).
doi: 10.1128/JB.182.3.771-781.2000
pubmed: 10633113
pmcid: 94342
Groisman, E. A. The pleiotropic two-component regulatory system PhoP-PhoQ. J. Bacteriol. 183, 1835–1842. https://doi.org/10.1128/JB.183.6.1835-1842.2001 (2001).
doi: 10.1128/JB.183.6.1835-1842.2001
pubmed: 11222580
pmcid: 95077
Schuhmacher, D. A. & Klose, K. E. Environmental signals modulate ToxT-dependent virulence factor expression in Vibrio cholerae. J. Bacteriol. 181, 1508–1514 (1999).
doi: 10.1128/JB.181.5.1508-1514.1999
pubmed: 10049382
pmcid: 93540
Hase, C. C. & Mekalanos, J. J. TcpP protein is a positive regulator of virulence gene expression in Vibrio cholerae. Proc. Natl. Acad. Sci. U. S. A. 95, 730–734 (1998).
doi: 10.1073/pnas.95.2.730
pubmed: 9435261
pmcid: 18489
DiRita, V. J. Co-ordinate expression of virulence genes by ToxR in Vibrio cholerae. Mol. Microbiol. 6, 451–458 (1992).
doi: 10.1111/j.1365-2958.1992.tb01489.x
pubmed: 1560773
Larsen, M. H. et al. Efficacy and safety of live attenuated persistent and rapidly cleared Mycobacterium tuberculosis vaccine candidates in non-human primates. Vaccine 27, 4709–4717. https://doi.org/10.1016/j.vaccine.2009.05.050 (2009).
doi: 10.1016/j.vaccine.2009.05.050
pubmed: 19500524
pmcid: 3512200
Sambandamurthy, V. K. et al. Long-term protection against tuberculosis following vaccination with a severely attenuated double lysine and pantothenate auxotroph of Mycobacterium tuberculosis. Infect. Immun. 73, 1196–1203. https://doi.org/10.1128/IAI.73.2.1196-1203.2005 (2005).
doi: 10.1128/IAI.73.2.1196-1203.2005
pubmed: 15664964
pmcid: 547051
Jain, P. et al. Specialized transduction designed for precise high-throughput unmarked deletions in Mycobacterium tuberculosis. mbio 5, e501245-01214. https://doi.org/10.1128/mBio.01245-14 (2014).
doi: 10.1128/mBio.01245-14
Cobbert, J. D. et al. Caught in action: selecting peptide aptamers against intrinsically disordered proteins in live cells. Sci. Rep. 5, 9402. https://doi.org/10.1038/srep09402 (2015).
doi: 10.1038/srep09402
pubmed: 25801767
pmcid: 4371151
Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108 (2008).
doi: 10.1038/nprot.2008.73
pubmed: 18546601
Roy, A., Kucukural, A. & Zhang, Y. I-TASSER: A unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725–738. https://doi.org/10.1038/nprot.2010.5 (2010).
doi: 10.1038/nprot.2010.5
pubmed: 20360767
pmcid: 2849174
Yang, J. et al. The I-TASSER suite: Protein structure and function prediction. Nat. Methods 12, 7–8. https://doi.org/10.1038/nmeth.3213 (2015).
doi: 10.1038/nmeth.3213
pubmed: 25549265
pmcid: 4428668
Zhang, Y. I-TASSER server for protein 3D structure prediction. BMC Bioinform. 9, 40. https://doi.org/10.1186/1471-2105-9-40 (2008).
doi: 10.1186/1471-2105-9-40
Datta, S., Ganesh, N., Chandra, N. R., Muniyappa, K. & Vijayan, M. Structural studies on MtRecA-nucleotide complexes: Insights into DNA and nucleotide binding and the structural signature of NTP recognition. Proteins 50, 474–485. https://doi.org/10.1002/prot.10315 (2003).
doi: 10.1002/prot.10315
pubmed: 12557189
Girardin, R. C. & McDonough, K. A. Small RNA Mcr11 requires the transcription factor AbmR for stable expression and regulates genes involved in the central metabolism of Mycobacterium tuberculosis. Mol. Microbiol. 113(2), 504–520. https://doi.org/10.1111/mmi.14436 (2020).