Adang MJ, Crickmore N, Jurat-Fuentes JL (2014) Diversity of Bacillus thuringiensis crystal toxins and mechanism of action. In: Dhadialla TS, Gill SS (eds) Advances in insect physiology. Elsevier, Amsterdam, Netherlands, pp 39–87
Amin N, McGrath A, Chen Y-PP (2019) Evaluation of deep learning in non-coding RNA classification. Nat Mach Intell 1:246–256. https://doi.org/10.1038/s42256-019-0051-2
Argôlo-Filho RC, Loguercio LL (2014) Bacillus thuringiensis is an environmental pathogen and host-specificity has developed as an adaptation to human-generated ecological niches. Insects 5:62–91. https://doi.org/10.3390/insects5010062
Bardou P, Mariette J, Escudié F et al (2014) Jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 15:1–7. https://doi.org/10.1186/1471-2105-15-293
Bazinet AL (2017) Pan-genome and phylogeny of Bacillus cereus sensu lato. BMC Evol Biol 17:1–16. https://doi.org/10.1186/s12862-017-1020-1
Cardoso P, Fazion F, Perchat S et al (2020) Rap-phr systems from plasmids pAW63 and pht8-1 act together to regulate sporulation in the Bacillus thuringiensis serovar kurstaki HD73 strain. Appl Environ Microbiol 86:1–16. https://doi.org/10.1128/AEM.01238-20
Carroll LM, Wiedmann M, Kovac J (2020) Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes. Mbio 11:1–15. https://doi.org/10.1101/779199
Chantsalnyam T, Lim DY, Tayara H, Chong KT (2020) ncRDeep: non-coding RNA classification with convolutional neural network. Comput Biol Chem 88:107364. https://doi.org/10.1016/j.compbiolchem.2020.107364
CAS Article PubMed Google Scholar
Chen Y, Indurthi DC, Jones SW, Papoutsakis E (2011) Small RNAs in the genus Clostridium. Mbio 2:1–11. https://doi.org/10.1128/mBio.00340-10
Crickmore N, Berry C, Panneerselvam S et al (2020) A structure-based nomenclature for Bacillus thuringiensis and other bacteria-derived pesticidal proteins. J Invertebr Pathol. https://doi.org/10.1016/j.jip.2020.107438
Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403. https://doi.org/10.1101/gr.2289704
CAS Article PubMed PubMed Central Google Scholar
Cardoso PdF, Perchat S, Vilas-Boas LA et al (2019) Diversity of the Rap-Phr quorum-sensing systems in the Bacillus cereus group. Curr Genet 65:1367–1381. https://doi.org/10.1007/s00294-019-00993-9
CAS Article PubMed Google Scholar
Drecktrah D, Hall LS, Brinkworth AJ et al (2020) Characterization of 6S RNA in the Lyme disease spirochete. Mol Microbiol 113:399–417. https://doi.org/10.1111/mmi.14427
CAS Article PubMed Google Scholar
Durand S, Braun F, Helfer AC et al (2017) sRNA-mediated activation of gene expression by inhibition of 5’-3’ exonucleolytic mRNA degradation. Elife 6:1–23. https://doi.org/10.7554/eLife.23602
Ehling-Schulz M, Fricker M, Grallert H et al (2006) Cereulide synthetase gene cluster from emetic Bacillus cereus: structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1. BMC Microbiol 6:1–11. https://doi.org/10.1186/1471-2180-6-20
Fayad N, Kallassy Awad M, Mahillon J (2019) Diversity of Bacillus cereus sensu lato mobilome. BMC Genomics 20:1–11. https://doi.org/10.1186/s12864-019-5764-4
Fazion F, Perchat S, Buisson C et al (2018) A plasmid-borne Rap-Phr system regulates sporulation of Bacillus thuringiensis in insect larvae. Environ Microbiol 20:145–155. https://doi.org/10.1111/1462-2920.13946
CAS Article PubMed Google Scholar
Fiannaca A, La Rosa M, La Paglia L et al (2017) nRC: non-coding RNA Classifier based on structural features. BioData Min 10:1–18. https://doi.org/10.1186/s13040-017-0148-2
Geissler AS, Anthon C, Alkan F et al (2021) Bsgatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. Microb Genomics 7:000524. https://doi.org/10.1099/mgen.0.000524
Geissmann T, Chevalier C, Cros MJ et al (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37:7239–7257. https://doi.org/10.1093/nar/gkp668
CAS Article PubMed PubMed Central Google Scholar
Gillis A, Fayad N, Makart L et al (2018) Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis. FEMS Microbiol Rev 42:829–856. https://doi.org/10.1093/femsre/fuy034
CAS Article PubMed PubMed Central Google Scholar
Gilois N, Ramarao N, Bouillaut L et al (2007) Growth-related variations in the Bacillus cereus secretome. Proteomics 7:1719–1728. https://doi.org/10.1002/pmic.200600502
CAS Article PubMed Google Scholar
Gripenland J, Netterling S, Loh E et al (2010) RNAs: regulators of bacterial virulence. Nat Rev Microbiol 8:857–866. https://doi.org/10.1038/nrmicro2457
CAS Article PubMed Google Scholar
Grissa I, Vergnaud G, Pourcel C (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8:1–10. https://doi.org/10.1186/1471-2105-8-172
Guillet J, Hallier M, Felden B (2013) Emerging functions for the Staphylococcus aureus RNome. PLoS Pathog 9:1–13. https://doi.org/10.1371/journal.ppat.1003767
Guinebretière MH, Thompson FL, Sorokin A et al (2008) Ecological diversification in the Bacillus cereus Group. Environ Microbiol 10:851–865. https://doi.org/10.1111/j.1462-2920.2007.01495.x
CAS Article PubMed Google Scholar
Harris KA, Breaker RR (2018) Large noncoding RNAs in bacteria. Microbiol Spectr 6:515–526. https://doi.org/10.1128/microbiolspec.rwr-0005-2017
Helgason E, Økstad OA, Dominique A et al (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis–one species on the basis of genetic evidence. Appl Environ Microbiol 66:2627–2630. https://doi.org/10.1128/AEM.66.6.2627-2630.2000
CAS Article PubMed PubMed Central Google Scholar
Hör J, Gorski SA, Vogel J (2018) Bacterial RNA biology on a genome scale. Mol Cell 70:785–799. https://doi.org/10.1016/j.molcel.2017.12.023
CAS Article PubMed Google Scholar
Irnov I, Sharma CM, Vogel J, Winkler WC (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38:6637–6651. https://doi.org/10.1093/nar/gkq454
CAS Article PubMed PubMed Central Google Scholar
Johnson M, Zaretskaya I, Raytselis Y et al (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:5–9. https://doi.org/10.1093/nar/gkn201
Jolley KA, Bray JE, Maiden MCJ (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:1–20. https://doi.org/10.12688/wellcomeopenres.14826.1
Kalvari I, Argasinska J, Quinones-Olvera N et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46:D335–D342. https://doi.org/10.1093/nar/gkx1038
CAS Article PubMed Google Scholar
Kolstø AB, Tourasse NJ, Økstad OA (2009) What sets Bacillus anthracis apart from other Bacillus species? Annu Rev Microbiol 63:451–476. https://doi.org/10.1146/annurev.micro.091208.073255
CAS Article PubMed Google Scholar
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Lee H, Zhang Z, Krause HM (2019) Long noncoding RNAs and repetitive elements: junk or intimate evolutionary partners? Trends Genet 35:892–902. https://doi.org/10.1016/j.tig.2019.09.006
CAS Article PubMed Google Scholar
Lehmann K, Schmidt U (2003) Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 38:249–303. https://doi.org/10.1080/713609236
CAS Article PubMed Google Scholar
Letunic I, Bork P (2019) Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:256–259. https://doi.org/10.1093/nar/gkz239
Li S, Hwang XY, Stav S, Breaker RR (2016) The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA 22:530–541. https://doi.org/10.1261/rna.054890.115
CAS Article PubMed PubMed Central Google Scholar
Liu Y, Lai Q, Göker M et al (2015) Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5:1–11. https://doi.org/10.1038/srep14082
Lu X, Liu SF, Yue L et al (2018) Epsc involved in the encoding of exopolysaccharides produced by Bacillus amyloliquefaciens FZB42 act to boost the drought tolerance of Arabidopsis thaliana. Int J Mol Sci 19:1–18. https://doi.org/10.3390/ijms19123795
Marincola G, Wencker F, Ziebuhr W (2019) The many facets of the small non-coding RNA RsaE (RoxS) in metabolic niche adaptation of gram-positive bacteria. J Mol Biol 431:4684–4698. https://doi.org/10.1016/j.jmb.2019.03.016
留言 (0)