References
- Costerton J.W., Lewandowski Z., Caldwell D.E., Korber D.R., Lappin-Scott H.M. Microbial biofilms. Annual Review of Microbiology. 1995;49:711–745. doi: 10.1146/annurev.mi.49.100195.003431
- Nikolaev Yu.A., Plakunov V.K. Biofilm-"City of Microbes" or an Analogue of Multicellular Organisms? Microbiology. 2007;76(2):125–138. doi: 10.1134/S0026261707020014
- Kaper J.B., Nataro J.P., Mobley H.L. Pathogenic Escherichia coli. Nature Reviews. Microbiology. 2004;2(2):123–140. doi: 10.1038/nrmicro818
- Wood T.K., Barrios A.F.G., Herzberg M., Lee J. Motility influences biofilm architecture in Escherichia coli. Applied Microbiology and Biotechnology. 2006;72(2):361–367. doi: 10.1007/s00253-005-0263-8
- Prüß B.M., Besemann C., Denton A., Wolfe A.J. A Complex Transcription Network Controls the Early Stages of Biofilm Development by Escherichia coli. Journal of bacteriology. 2006;188(11):3731–3739. doi: 10.1128/JB.01780-05
- Beloin C., Valle J., Latour-Lambert P., Faure P., Kzreminski M., Balestrino D., Haagensen J.A.J., Molin S., Prensier G., Arbeille B., Ghigo J.-M. Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression. Molecular Microbiology. 2004;51(3):659–674. doi: 10.1046/j.1365-2958.2003.03865.x
- Pratt L.A., Kolter R. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Molecular Microbiology. 1998;30(2):285–293. doi: 10.1046/j.1365-2958.1998.01061.x
- Hammar M., Bian Z., Normark S. Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 1996;93(13):6562–6566. doi: 10.1073/pnas.93.13.6562
- Bertin P., Terao E., Lee E.H., Lejeune P., Colson C., Danchin A., Collatz E. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. Journal of Bacteriology. 1994;176(17):5537–5540. doi: 10.1073/pnas.93.13.6562
- Jackson D.W., Simecka J.W., Romeo T. Catabolite repression of Escherichia coli biofilm formation. Journal of Bacteriology. 2002;184(12):3406–10. doi: 10.1128/JB.184.12.3406-3410.2002
- Wang X., Preston J.F., Romeo T. The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. Journal of Bacteriology. 2004;184(9):2724–2734. doi: 10.1128/JB.186.9.2724-2734.2004
- Gudapaty S., Suzuki K., Wang X., Babitzke P., Romeo T. Regulatory interactions of Csr components: the RNA binding protein CsrA activates csrB transcription in Escherichia coli. Journal of Bacteriology. 2001;183(20):6017–6027. doi: 10.1128/JB.183.20.6017-6027.2001
- Wang X., Dubey A.K., Suzuki K., Baker C.S., Babitzke P., Romeo T. CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli. Molecular Microbiology. 2005;56(6):1648–1663. doi: 10.1111/j.1365-2958.2005.04648.x
- Mizuno T., Chou M.Y., Inouye M. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proceedings of the National Academy of Sciences of the United States of America. 1984;81(7):1966–1970. doi: 10.1073/pnas.81.7.1966
- Wassarman K.M., Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell. 2000;101(6):613–623. doi: 10.1016/S0092-8674(00)80873-9
- Urban J.H., Vogel J. Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biology. 2008;6(3):e64. doi: 10.1371/journal.pbio.0060064
- Kulesus R.R., Diaz-Perez K., Slechta E.S., Eto D.S., Mulvey M.A. Impact of the RNA chaperone Hfq on the fitness and virulence potential of uropathogenic Escherichia coli. Infection and Immunity. 2008;76(7):3019–3026. doi: 10.1128/IAI.00022-08
- Jia T., Wu P., Liu B., Liu M., Mu H., Liu D., Huang M., Li L., Wei Y., Wang L., Yang Q., Liu Y., Yang B., Huang D., Yang L., Liu B. The phosphate-induced small RNA EsrL promotes E. coli virulence, biofilm formation, and intestinal colonization. Science Signaling. 2023;16(767):eabm0488. doi: 10.1126/scisignal.abm0488
- Ritzenthaler P., Mata-Gilsinger M. Use of in vitro gene fusions to study the uxuR regulatory gene in Escherichia coli K-12: direction of transcription and regulation of its expression. Journal of Bacteriology. 1982;150(3):1040–1047. doi: 10.1128/jb.150.3.1040-1047.1982
- Tutukina M.N., Dakhnovets A.I., Kaznadzey A.D., Gelfand M.S., Ozoline O.N. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Frontiers in Molecular Biosciences. 2023;10:1121376. doi: 10.3389/fmolb.2023.1121376
- Reed J.L., Patel T.R., Chen K.H., Joyce A.R., Applebee M.K., Herring C.D., Bui O.T., Knight E.M., Fong S.S., Palsson B.O. Systems approach to refining genome annotation. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(46):17480–17484. doi: 10.1073/pnas.0603364103
- Bessonova T.A., Kuznetsova U.D., Magkaev A.T., Gelfand M.S., Ozoline O.N., Tutukina M.N. Connection between hexuronate metabolism and the ability of Escherichia coli to adhesion and biofilm formation. Microbiology. 2024;93(4):497–501. doi: 10.1134/S002626172460472X
- NCBI RefSeq. https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/ (accessed 10 December 2024).
- FastQC. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed 10 December 2024).
- Trim Galore. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (accessed 10 December 2024).
- Langmead B., Salzberg S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923
- SAMtools. https://samtools.sourceforge.net/ (accessed 10 December 2024).
- Subread package. https://samtools.sourceforge.net/ (accessed 10 December 2024).
- Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15(550). doi: 10.1186/s13059-014-0550-8
- Gu Z., Eils R., Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32(18):2847–2849. doi: 10.1093/bioinformatics/btw313
- Monier B., McDermaid A., Zhao J., Ma Q. vidger: Create rapid visualizations of RNAseq data in R. R package version 1.26.0. 2024. https://bioconductor.org/packages/release/bioc/html/vidger.html, https://github.com/btmonier/vidger (accessed 10 December 2024).
- RColorBrewer. https://cran.r-project.org/web/packages/RColorBrewer/index.html (accessed 10 December 2024).
- circlize. https://cran.r-project.org/web/packages/circlize/index.html (accessed 10 December 2024).
- gplots. https://cran.r-project.org/web/packages/gplots/index.html (accessed 10 December 2024).
- Kopylova E., Noé L., Touzet H., SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28(24):3211–3217. doi: 10.1093/bioinformatics/bts611
- Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glöckner F.O. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research. 2013;41(D1):D590–D596. doi: 10.1093/nar/gks1219
- STAR (v2.7.11b). https://github.com/alexdobin/STAR (accessed 10 December 2024).
- Wassarman K.M., Storz G., 6S RNA regulates E. coli RNA polymerase activity. Cell. 2000;101(6):613–623. doi: 10.1016/S0092-8674(00)80873-9
- Benhalevy D., Bochkareva E.S., Biran I., Bibi E., Model Uracil-Rich RNAs and Membrane Protein mRNAs Interact Specifically with Cold Shock Proteins in Escherichia coli. PLoS One. 2015;10(7). Article No. e0134413. doi: 10.1371/journal.pone.0134413
|
|
|