{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:41:32Z","timestamp":1792593692099,"version":"4.5.0"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s10142-026-02084-8","type":"journal-article","created":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T02:01:58Z","timestamp":1792548118000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-wide identification and characterization of the PE\/PPE gene family in Mycobacterium abscessus"],"prefix":"10.1007","volume":"26","author":[{"given":"Panqi","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longxiang","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quanxin","family":"Long","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,21]]},"reference":[{"key":"2084_CR1","first-page":"34","volume":"46","author":"A Abudukadier","year":"2024","unstructured":"Abudukadier A, Zhang QA, Li PB, Xie JP (2024) Regulation of Mycobacterium biofilm development and novel measures against antibiotics resistance. Yi Chuan 46:34\u201345","journal-title":"Yi Chuan"},{"key":"2084_CR2","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.biochi.2011.09.026","volume":"94","author":"Y Akhter","year":"2012","unstructured":"Akhter Y, Ehebauer MT, Mukhopadhyay S, Hasnain SE (2012) The PE\/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more? Biochimie 94:110\u2013116","journal-title":"Biochimie"},{"key":"2084_CR3","doi-asserted-by":"publisher","first-page":"e0337624","DOI":"10.1128\/mbio.03376-24","volume":"16","author":"C Akusobi","year":"2025","unstructured":"Akusobi C, Choudhery S, Benghomari BS, Wolf ID, Singhvi S, Ioerger TR, Rubin EJ (2025) Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains. mBio 16:e0337624","journal-title":"mBio"},{"key":"2084_CR4","doi-asserted-by":"publisher","first-page":"40","DOI":"10.3389\/fcimb.2020.00040","volume":"10","author":"MK Ali","year":"2020","unstructured":"Ali MK, Zhen G, Nzungize L, Stojkoska A, Duan X, Li C, Duan W, Xu J, Xie J (2020) Mycobacterium tuberculosis PE31 (Rv3477) Attenuates Host Cell Apoptosis and Promotes Recombinant M. smegmatis Intracellular Survival via Up-regulating GTPase Guanylate Binding Protein-1. Front Cell Infect Microbiol 10:40","journal-title":"Front Cell Infect Microbiol"},{"key":"2084_CR5","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1007\/s00284-023-03360-7","volume":"80","author":"PK Anand","year":"2023","unstructured":"Anand PK, Kaur J (2023) Rv3539 (PPE63) of Mycobacterium Tuberculosis Promotes Survival of Mycobacterium Smegmatis in Human Macrophages Cell Line via Cell Wall Modulation of Bacteria and Altering Host\u2019s Immune Response. Curr Microbiol 80:267","journal-title":"Curr Microbiol"},{"key":"2084_CR7","doi-asserted-by":"publisher","first-page":"125837","DOI":"10.1016\/j.ijbiomac.2023.125837","volume":"247","author":"PK Anand","year":"2023","unstructured":"Anand PK, Saini V, Kaur J, Kumar A, Kaur J (2023a) Cell wall and immune modulation by Rv1800 (PPE28) helps M. smegmatis to evade intracellular killing. Int J Biol Macromol 247:125837","journal-title":"Int J Biol Macromol"},{"key":"2084_CR6","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.biochi.2023.05.004","volume":"213","author":"PK Anand","year":"2023","unstructured":"Anand PK, Kaur G, Saini V, Kaur J, Kaur J (2023b) N-terminal PPE domain plays an integral role in extracellular transportation and stability of the immunomodulatory Rv3539 protein of the Mycobacterium tuberculosis. Biochimie 213:30\u201340","journal-title":"Biochimie"},{"key":"2084_CR8","doi-asserted-by":"publisher","first-page":"1692","DOI":"10.1002\/pro.451","volume":"19","author":"MA Arbing","year":"2010","unstructured":"Arbing MA, Kaufmann M, Phan T, Chan S, Cascio D, Eisenberg D (2010) The crystal structure of the Mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer. Protein Sci 19:1692\u20131703","journal-title":"Protein Sci"},{"key":"2084_CR9","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"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\u201336","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"2084_CR10","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1128\/IAI.02032-14","volume":"83","author":"NG Bakala","year":"2015","unstructured":"Bakala NG, Le Moigne JC, Soismier V, Laencina N, Le Chevalier L, Roux F, Poncin AL, Serveau-Avesque I, Rottman C, Gaillard M, Etienne JL, Brosch G, Herrmann R, Canaan JL, Girard-Misguich S F (2015) Mycobacterium abscessus phospholipase C expression is induced during coculture within amoebae and enhances M. abscessus virulence in mice. Infect Immun 83:780\u2013791","journal-title":"Infect Immun"},{"key":"2084_CR11","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1038\/s41598-025-31168-x","volume":"16","author":"T Ballim","year":"2025","unstructured":"Ballim T, Mpye KL, Khoza T, Seele PP (2025) An in silico approach for screening non-synonymous SNPs in Mycobacterium tuberculosis PPE68 protein and impact on structure. Sci Rep 16:1407","journal-title":"Sci Rep"},{"key":"2084_CR12","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/S0966-842X(02)02335-1","volume":"10","author":"MJ Brennan","year":"2002","unstructured":"Brennan MJ, Delogu G (2002) The PE multigene family: a \u2018molecular mantra\u2019 for mycobacteria. Trends Microbiol 10:246\u2013249","journal-title":"Trends Microbiol"},{"key":"2084_CR13","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","volume":"16","author":"C Chen","year":"2023","unstructured":"Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, Xia R (2023) TBtools-II: A one for all, all for one bioinformatics platform for biological big-data mining. Mol Plant 16:1733\u20131742","journal-title":"Mol Plant"},{"key":"2084_CR14","doi-asserted-by":"crossref","unstructured":"Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537\u2013544","DOI":"10.1038\/31159"},{"key":"2084_CR15","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1186\/s12864-021-07670-7","volume":"22","author":"F Cornejo-Granados","year":"2021","unstructured":"Cornejo-Granados F, Kohl TA, Sotomayor FV, Andres S, Hern\u00e1ndez-Pando R, Hurtado-Ramirez JM, Utpatel C, Niemann S, Maurer FP, Ochoa-Leyva A (2021) Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences. BMC Genomics 22:385","journal-title":"BMC Genomics"},{"key":"2084_CR16","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/1756-0500-1-110","volume":"1","author":"A Cubillos-Ruiz","year":"2008","unstructured":"Cubillos-Ruiz A, Morales J, Zambrano MM (2008) Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments. BMC Res Notes 1:110","journal-title":"BMC Res Notes"},{"key":"2084_CR17","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.resmic.2017.10.001","volume":"169","author":"JL da Silva","year":"2018","unstructured":"da Silva JL, Nguyen J, Fennelly KP, Zelazny AM, Olivier KN (2018) Survival of pathogenic Mycobacterium abscessus subsp. massiliense in Acanthamoeba castellanii. Res Microbiol 169:56\u201360","journal-title":"Res Microbiol"},{"key":"2084_CR18","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/s42003-025-07572-4","volume":"8","author":"W Daher","year":"2025","unstructured":"Daher W, Le Moigne V, Tasrini Y, Parmar S, Sexton DL, Aguilera-Correa JJ, Berdal V, Tocheva EI, Herrmann JL, Kremer L (2025) Deletion of ESX-3 and ESX-4 secretion systems in Mycobacterium abscessus results in highly impaired pathogenicity. Commun Biol 8:166","journal-title":"Commun Biol"},{"key":"2084_CR19","doi-asserted-by":"publisher","first-page":"150927","DOI":"10.1016\/j.bbrc.2024.150927","volume":"739","author":"P Dahiya","year":"2024","unstructured":"Dahiya P, Banerjee A, Saha A, Nandicoori VK, Ghosh S, Mukhopadhyay S (2024) Structure-function relationship of PE11 esterase of Mycobacterium tuberculosis with respect to its role in virulence. Biochem Biophys Res Commun 739:150927","journal-title":"Biochem Biophys Res Commun"},{"key":"2084_CR20","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1080\/21505594.2020.1785815","volume":"11","author":"F De Maio","year":"2020","unstructured":"De Maio F, Berisio R, Manganelli R, Delogu G (2020) PE_PGRS proteins of Mycobacterium tuberculosis: A specialized molecular task force at the forefront of host-pathogen interaction. Virulence 11:898\u2013915","journal-title":"Virulence"},{"key":"2084_CR21","doi-asserted-by":"publisher","first-page":"e1008069","DOI":"10.1371\/journal.ppat.1008069","volume":"15","author":"V Dubois","year":"2019","unstructured":"Dubois V, Pawlik A, Bories A, Le Moigne V, Sismeiro O, Legendre R, Varet H, Rodr\u00edguez-Ord\u00f3\u00f1ez MDP, Gaillard JL, Copp\u00e9e JY, Brosch R, Herrmann JL, Girard-Misguich F (2019) Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages. PLoS Pathog 15:e1008069","journal-title":"PLoS Pathog"},{"key":"2084_CR22","doi-asserted-by":"publisher","first-page":"1517822","DOI":"10.3389\/fimmu.2025.1517822","volume":"16","author":"A Ehtram","year":"2025","unstructured":"Ehtram A, Shariq M, Quadir N, Jamal S, Pichipalli M, Zarin S, Sheikh JA, Ehtesham NZ, Hasnain SE (2025) Deciphering the functional roles of PE18 and PPE26 proteins in modulating Mycobacterium tuberculosis pathogenesis and immune response. Front Immunol 16:1517822","journal-title":"Front Immunol"},{"key":"2084_CR23","doi-asserted-by":"publisher","first-page":"842017","DOI":"10.3389\/fmicb.2022.842017","volume":"13","author":"KC Ferrell","year":"2022","unstructured":"Ferrell KC, Johansen MD, Triccas JA, Counoupas C (2022) Virulence Mechanisms of Mycobacterium abscessus: Current Knowledge and Implications for Vaccine Design. Front Microbiol 13:842017","journal-title":"Front Microbiol"},{"key":"2084_CR24","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1111\/mmi.12981","volume":"96","author":"S Fishbein","year":"2015","unstructured":"Fishbein S, van Wyk N, Warren RM, Sampson SL (2015) Phylogeny to function: PE\/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. Mol Microbiol 96:901\u2013916","journal-title":"Mol Microbiol"},{"key":"2084_CR28","doi-asserted-by":"publisher","first-page":"1244319","DOI":"10.3389\/fmicb.2023.1244319","volume":"14","author":"PJ G\u00f3mez-Gonz\u00e1lez","year":"2023","unstructured":"G\u00f3mez-Gonz\u00e1lez PJ, Grabowska AD, Tientcheu LD, Tsolaki AG, Hibberd ML, Campino S, Phelan JE, Clark TG (2023) Functional genetic variation in pe\/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. Front Microbiol 14:1244319","journal-title":"Front Microbiol"},{"key":"2084_CR26","doi-asserted-by":"crossref","unstructured":"Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, Holland SM, Horsburgh R, Huitt G, Iademarco MF, Iseman M, Olivier K, Ruoss S, von Reyn CF, Wallace RJ Jr, Winthrop K, ATS Mycobacterial Diseases Subcommittee (2007), American Thoracic Society, Infectious Disease Society of America An official ATS\/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175:367\u2013416","DOI":"10.1164\/rccm.200604-571ST"},{"key":"2084_CR27","doi-asserted-by":"publisher","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","volume":"8","author":"S Gupta","year":"2007","unstructured":"Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8:R24","journal-title":"Genome Biol"},{"key":"2084_CR29","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/s41579-020-0331-1","volume":"18","author":"MD Johansen","year":"2020","unstructured":"Johansen MD, Herrmann JL, Kremer L (2020) Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus. Nat Rev Microbiol 18:392\u2013407","journal-title":"Nat Rev Microbiol"},{"key":"2084_CR30","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, \u017d\u00eddek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583\u2013589","journal-title":"Nature"},{"key":"2084_CR31","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.tube.2010.09.006","volume":"91","author":"A Kapopoulou","year":"2011","unstructured":"Kapopoulou A, Lew JM, Cole ST (2011) The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes. Tuberculosis (Edinb) 91:8\u201313","journal-title":"Tuberculosis (Edinb)"},{"key":"2084_CR32","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.3390\/antibiotics13121151","volume":"13","author":"K Kraus","year":"2024","unstructured":"Kraus K, Mikzi\u0144ski P, Widelski J, Paluch E (2024) Prevention and Modern Strategies for Managing Methicillin-Resistant Staphylococcal Infections in Prosthetic Joint Infections (PJIs). Antibiot (Basel) 13:1151","journal-title":"Antibiot (Basel)"},{"key":"2084_CR33","doi-asserted-by":"publisher","first-page":"msae263","DOI":"10.1093\/molbev\/msae263","volume":"41","author":"S Kumar","year":"2024","unstructured":"Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, Tamura K (2024) MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. Mol Biol Evol 41:msae263","journal-title":"Mol Biol Evol"},{"key":"2084_CR34","doi-asserted-by":"publisher","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","volume":"15","author":"CW Law","year":"2014","unstructured":"Law CW, Chen Y, Shi W, Smyth GK (2014) voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15:R29","journal-title":"Genome Biol"},{"key":"2084_CR35","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P (2024) Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 52:W78\u2013W82","journal-title":"Nucleic Acids Res"},{"key":"2084_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.tube.2010.09.008","volume":"91","author":"JM Lew","year":"2011","unstructured":"Lew JM, Kapopoulou A, Jones LM, Cole ST (2011) TubercuList\u201310 years after. Tuberculosis (Edinb) 91:1\u20137","journal-title":"Tuberculosis (Edinb)"},{"key":"2084_CR37","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/s44259-024-00042-7","volume":"2","author":"Y Liu","year":"2024","unstructured":"Liu Y, Murphy K, Fernandes N, Moore RET, Pennisi I, Williams R, Rehk\u00e4mper M, Larrouy-Maumus G (2024) Transition metal homoeostasis is key to metabolism and drug tolerance of Mycobacterium abscessus. NPJ Antimicrob Resist 2:25","journal-title":"NPJ Antimicrob Resist"},{"key":"2084_CR38","doi-asserted-by":"publisher","first-page":"90","DOI":"10.3390\/microorganisms7030090","volume":"7","author":"RC Lopeman","year":"2019","unstructured":"Lopeman RC, Harrison J, Desai M, Cox JAG (2019) Mycobacterium abscessus: Environmental Bacterium Turned Clinical Nightmare. Microorganisms 7:90","journal-title":"Microorganisms"},{"key":"2084_CR39","doi-asserted-by":"publisher","first-page":"e0297024","DOI":"10.1128\/mbio.02970-24","volume":"15","author":"S Malmsheimer","year":"2024","unstructured":"Malmsheimer S, Daher W, Tasrini Y, Hamela C, Aguilera-Correa JJ, Chalut C, Hatfull GF, Kremer L (2024) Trehalose polyphleates participate in Mycobacterium abscessus fitness and pathogenesis. mBio 15:e0297024","journal-title":"mBio"},{"key":"2084_CR40","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1186\/s12864-016-2828-6","volume":"17","author":"AA Miranda-CasoLuengo","year":"2016","unstructured":"Miranda-CasoLuengo AA, Staunton PM, Dinan AM, Lohan AJ, Loftus BJ (2016) Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence. BMC Genomics 17:553","journal-title":"BMC Genomics"},{"key":"2084_CR41","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1007\/s11908-018-0611-3","volume":"20","author":"EA Misch","year":"2018","unstructured":"Misch EA, Saddler C, Davis JM (2018) Skin and Soft Tissue Infections Due to Nontuberculous Mycobacteria. Curr Infect Dis Rep 20:6","journal-title":"Curr Infect Dis Rep"},{"key":"2084_CR42","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","volume":"49","author":"J Mistry","year":"2021","unstructured":"Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A (2021) Pfam: The protein families database in 2021. Nucleic Acids Res 49:D412\u2013D419","journal-title":"Nucleic Acids Res"},{"key":"2084_CR43","doi-asserted-by":"publisher","first-page":"btae677","DOI":"10.1093\/bioinformatics\/btae677","volume":"40","author":"J Moreno","year":"2024","unstructured":"Moreno J, Nielsen H, Winther O, Teufel F (2024) Predicting the subcellular location of prokaryotic proteins with DeepLocPro. Bioinformatics 40:btae677","journal-title":"Bioinformatics"},{"key":"2084_CR44","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1007\/s00253-023-12420-8","volume":"107","author":"MMR Pereira","year":"2023","unstructured":"Pereira MMR, de Oliveira FM, da Costa AC, Junqueira-Kipnis AP, Kipnis A (2023) Ferritin from Mycobacterium abscessus is involved in resistance to antibiotics and oxidative stress. Appl Microbiol Biotechnol 107:2577\u20132595","journal-title":"Appl Microbiol Biotechnol"},{"key":"2084_CR45","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/s12864-016-3327-5","volume":"17","author":"JE Phelan","year":"2016","unstructured":"Phelan JE, Coll F, Bergval I, Anthony RM, Warren R, Sampson SL, van Gey NC, Glynn JR, Crampin AC, Alves A, Bessa TB, Campino S, Dheda K, Grandjean L, Hasan R, Hasan Z, Miranda A, Moore D, Panaiotov S, Perdigao J, Portugal I, Sheen P, de Oliveira Sousa E, Streicher EM, van Helden PD, Viveiros M, Hibberd ML, Pain A, McNerney R, Clark TG (2016) Recombination in pe\/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics 17:151","journal-title":"BMC Genomics"},{"key":"2084_CR46","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1186\/s13059-025-03854-6","volume":"26","author":"U Pozzoli","year":"2025","unstructured":"Pozzoli U, Forni D, Arrigoni F, Cagliani R, De Gioia L, Sironi M (2025) Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors. Genome Biol 26:387","journal-title":"Genome Biol"},{"key":"2084_CR47","doi-asserted-by":"publisher","first-page":"e5660","DOI":"10.1371\/journal.pone.0005660","volume":"4","author":"F Ripoll","year":"2009","unstructured":"Ripoll F, Pasek S, Schenowitz C, Dossat C, Barbe V, Rottman M, Macheras E, Heym B, Herrmann JL, Daff\u00e9 M, Brosch R, Risler JL, Gaillard JL (2009) Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS ONE 4:e5660","journal-title":"PLoS ONE"},{"key":"2084_CR48","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47","journal-title":"Nucleic Acids Res"},{"key":"2084_CR49","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406\u2013425","journal-title":"Mol Biol Evol"},{"key":"2084_CR50","doi-asserted-by":"publisher","first-page":"e00394","DOI":"10.1128\/IAI.00394-18","volume":"86","author":"P Santucci","year":"2018","unstructured":"Santucci P, Diomand\u00e9 S, Poncin I, Alibaud L, Viljoen A, Kremer L, de Chastellier C, Canaan S (2018) Delineating the Physiological Roles of the PE and Catalytic Domains of LipY in Lipid Consumption in Mycobacterium-Infected Foamy Macrophages. Infect Immun 86:e00394\u2013e00318","journal-title":"Infect Immun"},{"key":"2084_CR51","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1186\/s12859-019-3042-8","volume":"20","author":"PM Staunton","year":"2019","unstructured":"Staunton PM, Miranda-CasoLuengo AA, Loftus BJ, Gormley IC (2019) BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus. BMC Bioinformatics 20:466","journal-title":"BMC Bioinformatics"},{"key":"2084_CR52","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.jbiotec.2015.09.041","volume":"232","author":"D Stazic","year":"2016","unstructured":"Stazic D, Vo\u00df B (2016) The complexity of bacterial transcriptomes. J Biotechnol 232:69\u201378","journal-title":"J Biotechnol"},{"key":"2084_CR53","doi-asserted-by":"publisher","first-page":"e55320","DOI":"10.1371\/journal.pone.0055320","volume":"8","author":"R Sultana","year":"2013","unstructured":"Sultana R, Vemula MH, Banerjee S, Guruprasad L (2013) The PE16 (Rv1430) of Mycobacterium tuberculosis is an esterase belonging to serine hydrolase superfamily of proteins. PLoS ONE 8:e55320","journal-title":"PLoS ONE"},{"key":"2084_CR54","doi-asserted-by":"publisher","first-page":"8024","DOI":"10.1038\/s41598-020-64895-4","volume":"10","author":"P Tantivitayakul","year":"2020","unstructured":"Tantivitayakul P, Ruangchai W, Juthayothin T, Smittipat N, Disratthakit A, Mahasirimongkol S, Viratyosin W, Tokunaga K, Palittapongarnpim P (2020) Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis. Sci Rep 10:8024","journal-title":"Sci Rep"},{"key":"2084_CR55","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1111\/j.1472-765X.2007.02206.x","volume":"45","author":"V Thomas","year":"2007","unstructured":"Thomas V, McDonnell G (2007) Relationship between mycobacteria and amoebae: ecological and epidemiological concerns. Lett Appl Microbiol 45:349\u2013357","journal-title":"Lett Appl Microbiol"},{"key":"2084_CR56","doi-asserted-by":"publisher","first-page":"11184","DOI":"10.1074\/jbc.RA120.013299","volume":"295","author":"L Thouvenel","year":"2020","unstructured":"Thouvenel L, Prevot G, Chiaradia L, Parra J, Mouton-Barbosa E, Locard-Paulet M, Marcoux J, Tropis M, Burlet-Schiltz O, Daff\u00e9 M, Guilhot C, Etienne G, Chalut C (2020) The final assembly of trehalose polyphleates takes place within the outer layer of the mycobacterial cell envelope. J Biol Chem 295:11184\u201311194","journal-title":"J Biol Chem"},{"key":"2084_CR57","doi-asserted-by":"publisher","first-page":"E348","DOI":"10.1073\/pnas.1523321113","volume":"113","author":"JM Tufariello","year":"2016","unstructured":"Tufariello JM, Chapman JR, Kerantzas CA, Wong KW, Vilch\u00e8ze C, Jones CM, Cole LE, Tinaztepe E, Thompson V, Feny\u00f6 D, Niederweis M, Ueberheide B, Philips JA, Jacobs WR Jr (2016) Separable roles for Mycobacterium tuberculosis ESX-3 effectors in iron acquisition and virulence. Proc Natl Acad Sci U S A 113:E348\u2013E357","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2084_CR58","doi-asserted-by":"publisher","first-page":"4110","DOI":"10.1073\/pnas.1419677112","volume":"112","author":"KH Turner","year":"2015","unstructured":"Turner KH, Wessel AK, Palmer GC, Murray JL, Whiteley M (2015) Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proc Natl Acad Sci U S A 112:4110\u20134115","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2084_CR25","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1186\/1471-2148-6-95","volume":"6","author":"NC van Gey","year":"2006","unstructured":"van Gey NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM (2006) Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol Biol 6:95","journal-title":"BMC Evol Biol"},{"key":"2084_CR59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1021\/bi052130w","volume":"45","author":"MW Vetting","year":"2006","unstructured":"Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS (2006) Pentapeptide repeat proteins. Biochemistry 45:1\u201310","journal-title":"Biochemistry"},{"key":"2084_CR61","doi-asserted-by":"crossref","unstructured":"Wang Q, Boshoff HIM, Harrison JR, Ray PC, Green SR, Wyatt PG, Barry CE 3rd (2020) PE\/PPE proteins mediate nutrient transport across the outer membrane of Mycobacterium tuberculosis. Science 367:1147\u20131151","DOI":"10.1126\/science.aav5912"},{"key":"2084_CR60","doi-asserted-by":"publisher","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","volume":"51","author":"J Wang","year":"2023","unstructured":"Wang J, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A (2023) The conserved domain database in 2023. Nucleic Acids Res 51:D384\u2013D388","journal-title":"Nucleic Acids Res"},{"key":"2084_CR62","doi-asserted-by":"publisher","first-page":"1360880","DOI":"10.3389\/fcimb.2024.1360880","volume":"14","author":"S Wang","year":"2024","unstructured":"Wang S, Fang R, Wang H, Li X, Xing J, Li Z, Song N (2024) The role of transcriptional regulators in metal ion homeostasis of Mycobacterium tuberculosis. Front Cell Infect Microbiol 14:1360880","journal-title":"Front Cell Infect Microbiol"},{"key":"2084_CR63","doi-asserted-by":"publisher","first-page":"S214","DOI":"10.1134\/S0006297924603496","volume":"90","author":"EV Zakhareva","year":"2025","unstructured":"Zakhareva EV, Martini BA, Salina EG (2025) Mechanisms of Virulence of Mycobacterium abscessus and Interaction with the Host Immune System. Biochem (Mosc) 90:S214\u2013S232","journal-title":"Biochem (Mosc)"},{"key":"2084_CR64","doi-asserted-by":"publisher","first-page":"1606311","DOI":"10.3389\/fimmu.2025.1606311","volume":"16","author":"Z Zhang","year":"2025","unstructured":"Zhang Z, Dong L, Li X, Deng T, Wang Q (2025) The PE\/PPE family proteins of Mycobacterium tuberculosis: evolution, function, and prospects for tuberculosis control. Front Immunol 16:1606311","journal-title":"Front Immunol"}],"container-title":["Functional &amp; Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-02084-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-026-02084-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-02084-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:02:07Z","timestamp":1792591327000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-026-02084-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,21]]},"references-count":64,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["2084"],"URL":"https:\/\/doi.org\/10.1007\/s10142-026-02084-8","relation":{},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,21]]},"assertion":[{"value":"23 July 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 October 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 October 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":3,"name":"Ethics","label":"Clinical trial number","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"296"}}