Lahiri A, Sanchini A, Semmler T, Schafer H, Lewin A (2014) Identification and comparative analysis of a genomic island in Mycobacterium avium subsp. hominissuis. FEBS Let 588(21):3906–3911. https://doi.org/10.1016/j.febslet.2014.08.037
Article
Google Scholar
Gonzalez-Perez MN, Murcia MI, Parra-Lopez C, Blom J, Tauch A (2016) Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense. New Microbe New Infect 14:98–105. https://doi.org/10.1016/j.nmni.2016.09.007
Article
Google Scholar
Maya-Hoyos M, Leguizamon J, Marino-Ramirez L, Soto CY (2015) Sliding motility, biofilm formation, and Glycopeptidolipid production in Mycobacterium colombiense strains. Biomed Res Int 2015:419549. https://doi.org/10.1155/2015/419549
Article
Google Scholar
Gcebe N, Hlokwe TM (2017) Non-tuberculous mycobacteria in south African wildlife: neglected pathogens and potential impediments for bovine tuberculosis diagnosis. Front Cell Infect Microbiol 7:15. https://doi.org/10.3389/fcimb.2017.00015
Article
Google Scholar
Gonzalez-Perez M, Marino-Ramirez L, Parra-Lopez CA, Murcia MI, Marquina B, Mata-Espinoza D (2013) Virulence and immune response induced by Mycobacterium avium complex strains in a model of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice. Infect Immun 81(11):4001–4012. https://doi.org/10.1128/IAI.00150-13
Article
Google Scholar
Nishiuchi Y, Iwamoto T, Maruyama F (2017) Infection sources of a common non-tuberculous mycobacterial pathogen, Mycobacterium avium complex. Front Med 4:27. https://doi.org/10.3389/fmed.2017.00027
Article
Google Scholar
Al-Mahruqi SH, van Ingen J, Al Busaidy S, Boeree MJ, Al Zadjali S, Patel A, Richard Dekhuijzen PN, van Soolingen D (2009) Clinical relevance of nontuberculous mycobacteria, Oman. Emerg Infect Dis 15(2):292–294. https://doi.org/10.3201/eid1502.080977
Article
Google Scholar
Baldwin SL, Larsen SE, Ordway D, Cassell G, Coler RN (2019) The complexities and challenges of preventing and treating nontuberculous mycobacterial diseases. PLoS Negl Trop Dis 13(2):e0007083. https://doi.org/10.1371/journal.pntd.0007083
Article
Google Scholar
Maurya AK, Nag VL, Kant S, Kushwaha RA, Kumar M, Singh AK, Dhole TN (2015) Prevalence of nontuberculous mycobacteria among extrapulmonary tuberculosis cases in tertiary care centers in northern India. Biomed Res Int 2015:465403. https://doi.org/10.1155/2015/465403
Article
Google Scholar
Sharma P, Singh D, Sharma K, Verma S, Mahajan S, Kanga A (2018) Are we neglecting nontuberculous mycobacteria just as laboratory contaminants? Time to reevaluate things. J Pathog 2018:8907629. https://doi.org/10.1155/2018/8907629
Article
Google Scholar
Gonzalez-Perez M, Murcia MI, Landsman D, Jordan IK, Marino-Ramírez L (2011) Genome sequence of the Mycobacterium colombiense type strain, CECT 3035. J Bacteriol 193(20):5866–5867. https://doi.org/10.1128/JB.05928-11
Article
Google Scholar
Maurer FP, Pohle P, Kernbach M et al (2019) Differential drug susceptibility patterns of Mycobacterium chimaera and other members of the Mycobacterium avium-intracellulare complex. Clin Microbiol Infect 25(3):371–379. https://doi.org/10.1016/j.cmi.2018.06.0108
Article
Google Scholar
Saxena S, Spaink HP, Forn-Cuni G (2021) Drug resistance in nontuberculous mycobacteria: mechanisms and models. Biology 10:96. https://doi.org/10.3390/biology10020096
Article
Google Scholar
Cuthbertson L, Nodwell JR (2013) The TetR family of regulators. Microbiol Mol Biol Rev 77(3):440–475. https://doi.org/10.1128/MMBR.00018-13
Article
Google Scholar
Colclough AL, Scadden J, Blair JMA (2019) TetR-family transcription factors in gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance. BMC Genomics 20:731. https://doi.org/10.1186/s12864-019-6075-5
Article
Google Scholar
Balhana RJ, Singla A, Sikder MH, Withers M, Kendall SL (2015) Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions. BMC Genomics 16(1):479. https://doi.org/10.1186/s12864-015-1696-9
Article
Google Scholar
Soutourina O, Dubois T, Monot M, Shelyakin PV, Saujet L, Boudry P, Gelfand MS, Dupuy B, Martin-Verstraete I (2020) Genome-wide transcription start site mapping and promoter assignments to a sigma factor in the human enteropathogen Clostridioides difficile. Front Microbiol 11(1939):1–24. https://doi.org/10.3389/fmicb.2020.01939
Article
Google Scholar
Reese MG, Harris NL, Eeckman FH (1996) Large scale sequencing specific neural networks for promoter and splice site recognition. In: Bio - computing: proceedings of the 1996 Pacific symposium, Singapore http://www.fruitfly.org/seq_tools/promoter.html
Google Scholar
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36 https://www.osti.gov/biblio/377124
Google Scholar
Bailey TL, Johnson J, Grant CE, Noble WS (2015) The MEME suite. Nucleic Acids Res 43(W1):39–49. https://doi.org/10.1093/nar/gkv416
Article
Google Scholar
Peng S, Cheng M, Huang K (2018) Efficient computation of motif discovery on Intel many integrated Core (MIC) architecture. BMC Bioinformatics 19(282):102–121. https://doi.org/10.1186/s12859-018-2276-1
Article
Google Scholar
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8:R24. https://doi.org/10.1186/gb-2007-8-2-r24
Article
Google Scholar
Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A 99:3740–3745. https://doi.org/10.1073/pnas.052410099
Article
Google Scholar
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Article
Google Scholar
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035. https://doi.org/10.1073/pnas.0404206101
Article
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Article
Google Scholar
Hall BG (2013) Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 30(5):1229–1235. https://doi.org/10.1093/molbev/mst012
Article
Google Scholar
Prados J, Linder P, Redder P (2016) TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens. BMC Genomics 17(1):849. https://doi.org/10.1186/s12864-016-3211-3
Article
Google Scholar
Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonean AC (2016) Global repositioning of transcription start sites in a plant-fermenting bacterium. Nat Commun 7(13783):1–9. https://doi.org/10.1038/ncomms13783
Article
Google Scholar
Jorjani H, Zavolan M (2014) TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics 30(7):971–974. https://doi.org/10.1093/bioinformatics/btt752
Article
Google Scholar
Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B et al (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 4(10):e7526. https://doi.org/10.1371/journal.pone.0007526
Article
Google Scholar
Umarov V, Solovyev R (2017) Prediction of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PLoS One 12:2. https://doi.org/10.1371/journal.pone.0171410
Article
Google Scholar
Richard M, Gutiérrez AV, Viljoen AJ, Ghigo E, Blaise M, Kremer L (2018) (2018) mechanistic and structural insights into the unique TetR-dependent regulation of a drug efflux pump in Mycobacterium abscessus. Front Microbiol 9:649. https://doi.org/10.3389/fmicb.2018.00649
Article
Google Scholar
Gordon JJ, Towsey MW, Hogan JM, Mathews SA, Timms P (2006) Improved prediction of bacterial transcription start sites. Bioinformatics 22(2):142–148. https://doi.org/10.1093/bioinformatics/bti771
Article
Google Scholar
Shin MK, Shin SJ (2021) Genetic involvement of Mycobacterium avium complex in the regulation and manipulation of innate immune functions of host cells. Int J Mol Sci 22:3011. https://doi.org/10.3390/ijms22063011
Article
Google Scholar
Falkinham JO III (2018) Challenges of NTM drug development. Front Microbiol 9:1613. https://doi.org/10.3389/fmicb.2018.01613
Article
Google Scholar
Huang Y, Chen Y, Zhang LH (2020) The roles of microbial cell-cell chemical communication systems in the modulation of antimicrobial resistance. Antibiotics (Basel) 9(11):779. https://doi.org/10.3390/antibiotics9110779
Article
Google Scholar
Faria S, Joao I, Jordao L (2015) General overview on nontuberculous mycobacteria, biofilms, and human infection. J Pathog 2015:809014. https://doi.org/10.1155/2015/809014
Article
Google Scholar
Simoes M (2011) Antimicrobial strategies effective against infectious bacterial biofilms. Curr Med Chem 18(14):2129–2145. https://doi.org/10.2174/092986711795656216
Article
Google Scholar
Dong YH, Zhang XF, Xu JL, Tan AT, Zhang LH (2005) VqsM, a novel AraC-type global regulator of quorum-sensing signalling and virulence in Pseudomonas aeruginosa. Mol Microbiol 58(2):552–564. https://doi.org/10.1111/j.1365-2958.2005.04851.x
Article
Google Scholar
Wang Y, Gao L, Rao X, Wang J, Yu H, Jiang J, Zhou W, Wang J, Xiao Y, Li M, Zhang Y, Zhang K, Shen L, Hua Z (2018) Characterization of lasR-deficient clinical isolates of Pseudomonas aeruginosa. Sci Rep 8(1):13344. https://doi.org/10.1038/s41598-018-30813-y
Article
Google Scholar
Lade H, Paul D, Kweon JH (2014) Quorum quenching mediated approaches for control of membrane biofouling Int. J Biol Sci 10(5):550–565. https://doi.org/10.7150/ijbs.9028
Article
Google Scholar
De Voss JJ, Rutter K, Schroeder BG, Su H, Zhu Y, Barry CE 3rd (2000) The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages. Proc Natl Acad Sci U S A 97(3):1252–1257. https://doi.org/10.1073/pnas.97.3.1252
Article
Google Scholar
Kopinˇc R, Lapanje A (2012) Antibiotic susceptibility profile of Mycobacterium avium subspecies hominissuis is altered in low-iron conditions. J Antimicrob Chemother 67(12):2903–2907. https://doi.org/10.1093/jac/dks313
Article
Google Scholar
Leoni L, Orsi N, Lorenzo V, Visca P (2000) Functional analysis of PvdS, an iron starvation sigma factor of Pseudomonas aeruginosa. J Bacteriol 182(6):1481–1491. https://doi.org/10.1128/JB.182.6.1481-1491.2000
Article
Google Scholar
Lizewski SE, Lundberg DS, Schurr MJ (2002) The transcriptional regulator AlgR is essential for Pseudomonas aeruginosa pathogenesis. Infect Immun 70(11):6083–6093. https://doi.org/10.1128/IAI.70.11.6083-6093.2002
Article
Google Scholar
Li Y, Xiao Y, Zou L, Chen G (2012) Identification of HrpX regulon genes in Xanthomonas oryzae pv. Oryzicola using a GFP visualization technique. Arch Microbiol 194(4):281–291. https://doi.org/10.1007/s00203-011-0758-x
Article
Google Scholar
Nguyen Le Minh P, de Cima S, Bervoets I, Maes D, Rubio V, Charlier D (2015) Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli. FEBS Open Bio 5:76–84. https://doi.org/10.1016/j.fob.2015.01.002
Article
Google Scholar
Lu CD, Yang Z, Li W (2004) Transcriptome analysis of the ArgR regulon in Pseudomanas aeruginosa. J Bacteriol 186(12):3855–3861. https://doi.org/10.1128/JB.186.12.3855-3861.2004
Article
Google Scholar
Silva-Rocha R, Chavarría M, Kleijn RJ, Sauer U, de Lorenzo V (2013) The IHF regulon of exponentially growing pseudomonas putida cells. Environ Microbiol 15(1):49–63. https://doi.org/10.1111/j.1462-2920.2012.02750.x
Article
Google Scholar
Mercier R, Petit MA, Schbath S, Karoui ME, Boccard F, Espeli O (2008) The MatP/mats site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135(3):475–485. https://doi.org/10.1016/j.cell.2008.08.031
Article
Google Scholar
Spencer W, Siam R, Ouimet MC, Bastedo DP, Marczynski GT (2009) CtrA, a global response regulator, uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus. J Bacteriol 191(17):5458–5470. https://doi.org/10.1128/JB.00355-09
Article
Google Scholar
Silber N, de Opitz CLM, Mayer C, Sass P (2020) Cell division protein Ftsz: from structure and mechanism to antibiotic target. Future Microbiol 15(9):348. https://doi.org/10.2217/fmb-2019-0348
Article
Google Scholar
Adikesavan AK, Katsonis P, Marciano DC, Lua R, Herman C, Lichtarge O (2011) Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet 7(9):1–14. https://doi.org/10.1371/journal.pgen.1002244
Article
Google Scholar
Mo CY, Manning SA, Roggiani M, Culyba MJ, Samuels AN, Sriegowski PD, Goulian M, Kohli RM (2016) Systematically altering bacterial SOS activity under stress reveals therapeutic strategies for potentiating antibiotics. mSphere 1(4):e00163–e00116. https://doi.org/10.1128/mSphere.00163-16
Article
Google Scholar
Kakumani R, Ahmad O, Devabhaktuni V (2012) Identification of CpG islands in DNA sequences using statistically optimal null filters. EURASTP J Bioinform Syst Biol 2012(1):12. https://doi.org/10.1186/1687-4153-2012-12
Article
Google Scholar
Lim WJ, Kim KH, Kim JY, Jeong S, Kim N (2019) Identification of DNA-methylated CpG islands associated with gene silencing in the adult body tissues of the Ogye chicken using RNA-Seq and reduced representation bisulfite sequencing. Front Genet 10:346. https://doi.org/10.3389/fgene.2019.00346
Article
Google Scholar
Yirgu M, Kebede M (2019) Analysis of the promoter region, motif and CpG islands in AraC family transcriptional regulator ACP92 genes of Herbaspirillum seropedicae. Adv Biosci Biotechnol 10:150–164. https://doi.org/10.4236/abb.2019.106011
Article
Google Scholar
Hershberg R, Petrov DA (2008) Selection on codon bias. Annu Rev Genet 42:287–299. https://doi.org/10.1146/annurev.genet.42.110807.091442
Article
Google Scholar
Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12:32–42. https://doi.org/10.1038/nrg2899
Article
Google Scholar
Murcia MI, Tortoli E, Menendez C, Palenque E, Garcia MJ (2006) Mycobacterium colombiense sp. nov., a novel member of the Mycobacterium avium complex and description of MAC-X as a new ITS genetic variant. Int J Syst Evol Microbiol 56(9):2049–2054. https://doi.org/10.1099/ijs.0.64190-0
Article
Google Scholar