{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:03:35Z","timestamp":1760144615546,"version":"build-2065373602"},"reference-count":45,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T00:00:00Z","timestamp":1713916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007917","name":"USDA-ARS","doi-asserted-by":"publisher","award":["58-6402-2-729","P20GM103476"],"award-info":[{"award-number":["58-6402-2-729","P20GM103476"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institutional Development Award (IDeA)","award":["58-6402-2-729","P20GM103476"],"award-info":[{"award-number":["58-6402-2-729","P20GM103476"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Listeria monocytogenes is the causative agent of listeriosis, a severe foodborne illness characterized by septicemia, meningitis, encephalitis, abortions, and occasional death in infants and immunocompromised individuals. L. monocytogenes is composed of four genetic lineages (I, II, III, and IV) and fourteen serotypes. The aim of the current study was to identify proteins that can serve as biomarkers for detection of genetic lineage III strains based on simple antibody-based methods. Liquid chromatography (LC) with electrospray ionization tandem mass spectrometry (ESI MS\/MS) followed by bioinformatics and computational analysis were performed on three L. monocytogenes strains (NRRL B-33007, NRRL B-33014, and NRRL B-33077), which were used as reference strains for lineages I, II, and III, respectively. Results from ESI MS\/MS revealed 42 unique proteins present in NRRL B-33077 and absent in NRRL B-33007 and NRRL B-33014 strains. BLAST analysis of the 42 proteins against a broader panel of &gt;80 sequenced strains from lineages I and II revealed four proteins [TM2 domain-containing protein (NRRL B-33077_2770), DUF3916 domain-containing protein (NRRL B-33077_1897), DNA adenine methylase (NRRL B-33077_1926), and protein RhsA (NRRL B-33077_1129)] that have no homology with any sequenced strains in lineages I and II. The four genes that encode these proteins were expressed in Escherichia coli strain DE3 and purified. Polyclonal antibodies were prepared against purified recombinant proteins. ELISA using the polyclonal antibodies against 12 L. monocytogenes lineage I, II, and III isolates indicated that TM2 protein and DNA adenine methylase (Dam) detected all lineage III strains with no reaction to lineage I and II strains. In conclusion, two proteins including TM2 protein and Dam are potentially useful biomarkers for detection and differentiation of L. monocytogenes lineage III strains in clinical, environmental, and food processing facilities. Furthermore, these results validate the approach of using a combination of proteomics and bioinformatics to identify useful protein biomarkers.<\/jats:p>","DOI":"10.3390\/foods13091302","type":"journal-article","created":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T03:56:31Z","timestamp":1713930991000},"page":"1302","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of Protein Biomarkers for Differentiating Listeria monocytogenes Genetic Lineage III"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-8829-1950","authenticated-orcid":false,"given":"Basant","family":"Gomaa","sequence":"first","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingjun","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hossam","family":"Abdelhamed","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle","family":"Banes","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga","family":"Pechanova","sequence":"additional","affiliation":[{"name":"Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tibor","family":"Pechan","sequence":"additional","affiliation":[{"name":"Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7207-3052","authenticated-orcid":false,"suffix":"II","given":"Mark A.","family":"Arick","sequence":"additional","affiliation":[{"name":"Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6845-3346","authenticated-orcid":false,"given":"Attila","family":"Karsi","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark L.","family":"Lawrence","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,4,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1128\/mr.55.3.476-511.1991","article-title":"Listeria monocytogenes, a food-borne pathogen","volume":"55","author":"Farber","year":"1991","journal-title":"Microbiol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1002\/path.1700290409","article-title":"A disease of rabbits characterised by a large mononuclear leucocytosis, caused by a hitherto undescribed bacillus Bacterium monocytogenes (n.sp.)","volume":"29","author":"Murray","year":"1926","journal-title":"J. Pathol. Bacteriol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1056\/NEJM198301273080407","article-title":"Epidemic Listeriosis\u2014Evidence for Transmission by Food","volume":"308","author":"Schlech","year":"1983","journal-title":"N. Engl. J. Med."},{"key":"ref_4","first-page":"851712","article-title":"Listeriosis during pregnancy: A public health concern","volume":"2013","author":"Mateus","year":"2013","journal-title":"Int. Sch. Res. Not."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1128\/CMR.14.3.584-640.2001","article-title":"Listeria pathogenesis and molecular virulence determinants","volume":"14","author":"Kuhn","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1111\/j.1365-2621.2001.00451.x","article-title":"Listeria, Listeriosis and Food Safety, 2nd edition","volume":"36","author":"Harrigan","year":"2001","journal-title":"Int. J. Food Sci. Technol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"844","DOI":"10.4315\/0362-028X-52.12.844","article-title":"Effects and Interactions of Temperature, pH, Atmosphere, Sodium Chloride, and Sodium Nitrite on the Growth of Listeria monocytogenes","volume":"52","author":"Buchanan","year":"1989","journal-title":"J. Food Prot."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.4102\/ojvr.v87i1.1869","article-title":"A review of Listeria monocytogenes from meat and meat products: Epidemiology, virulence factors, antimicrobial resistance and diagnosis","volume":"87","author":"Matle","year":"2020","journal-title":"Onderstepoort J. Vet. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1111\/jam.12876","article-title":"Identification of high-risk Listeria monocytogenes serotypes in lineage I (serotype 1\/2a, 1\/2c, 3a and 3c) using multiplex PCR","volume":"119","author":"Nho","year":"2015","journal-title":"J. Appl. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2704","DOI":"10.1128\/JCM.39.7.2704-2707.2001","article-title":"Correlations between Molecular Subtyping and Serotyping of Listeria monocytogenes","volume":"39","author":"Nadon","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1099\/13500872-141-9-2053","article-title":"Listeria monocytogenes exists in at least three evolutionary lines: Evidence from flagellin, invasive associated protein and listeriolysin O genes","volume":"141","author":"Rasmussen","year":"1995","journal-title":"Microbiology"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"6680","DOI":"10.1128\/AEM.01008-10","article-title":"A targeted multilocus genotyping assay for lineage, serogroup, and epidemic clone typing of Listeria monocytogenes","volume":"76","author":"Ward","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kuenne, C., Billion, A., Mraheil, M.A., Strittmatter, A., Daniel, R., Goesmann, A., Barbuddhe, S., Hain, T., and Chakraborty, T. (2013). Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-47"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1128\/AEM.68.2.616-622.2002","article-title":"Expression of ActA, Ami, InlB, and listeriolysin O in Listeria monocytogenes of human and food origin","volume":"68","author":"Jacquet","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1017\/S0950268805005376","article-title":"Nationwide outbreak of listeriosis due to contaminated meat","volume":"134","author":"Mead","year":"2005","journal-title":"Epidemiol. Infect."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5846","DOI":"10.1128\/AEM.00816-09","article-title":"Competition of Listeria monocytogenes serotype 1\/2a and 4b strains in mixed-culture biofilms","volume":"75","author":"Pan","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5537","DOI":"10.1128\/JCM.41.12.5537-5540.2003","article-title":"Listeria monocytogenes serotype identification by PCR","volume":"41","author":"Borucki","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.4315\/0362-028X-70.7.1569","article-title":"Variable adhesion of Listeria monocytogenes isolates from food-processing facilities and clinical cases to inert surfaces","volume":"70","author":"Tresse","year":"2007","journal-title":"J. Food Prot."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.4315\/0362-028X-67.11.2488","article-title":"Strain-specific differences in the attachment of Listeria monocytogenes to alfalfa sprouts","volume":"67","author":"Gorski","year":"2004","journal-title":"J. Food Prot."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1128\/AEM.69.1.258-266.2003","article-title":"Attachment of Listeria monocytogenes to radish tissue is dependent upon temperature and flagellar motility","volume":"69","author":"Gorski","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1104\/pp.81.3.802","article-title":"Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis","volume":"81","author":"Hurkman","year":"1986","journal-title":"Plant Physiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.vetmic.2016.10.026","article-title":"Protective efficacy of four recombinant fimbrial proteins of virulent Aeromonas hydrophila strain ML09-119 in channel catfish","volume":"197","author":"Abdelhamed","year":"2016","journal-title":"Vet. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0168-1605(99)00057-4","article-title":"Genomic typing of Listeria monocytogenes strains by automated laser fluorescence analysis of amplified fragment length polymorphism fingerprint patterns","volume":"49","author":"Aarts","year":"1999","journal-title":"Int. J. Food Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Aguilar-Bultet, L., Nicholson, P., Rychener, L., Dreyer, M., Gozel, B., Origgi, F.C., Oevermann, A., Frey, J., and Falquet, L. (2018). Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals. Front. Cell. Infect. Microbiol., 8.","DOI":"10.3389\/fcimb.2018.00020"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1128\/aem.56.7.2133-2141.1990","article-title":"Analysis of clinical and food-borne isolates of Listeria monocytogenes in the United States by multilocus enzyme electrophoresis and application of the method to epidemiologic investigations","volume":"56","author":"Bibb","year":"1990","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3818","DOI":"10.1073\/pnas.86.10.3818","article-title":"Genetic characterization of clones of the bacterium Listeria monocytogenes causing epidemic disease","volume":"86","author":"Piffaretti","year":"1989","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1586\/erm.10.17","article-title":"DNA methylation as a universal biomarker","volume":"10","author":"Levenson","year":"2010","journal-title":"Expert Rev. Mol. Diagn."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1007\/s13361-012-0508-6","article-title":"Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS\/MS of complex proteomic samples","volume":"24","author":"Hsieh","year":"2013","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1021\/pr500882h","article-title":"Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome","volume":"14","author":"Wang","year":"2015","journal-title":"J. Proteome Res."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Jakobsdottir, J., van der Lee, S.J., Bis, J.C., Chouraki, V., Li-Kroeger, D., Yamamoto, S., Grove, M.L., Naj, A., Vronskaya, M., and Salazar, J.L. (2016). Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer\u2019s Disease. PLOS Genet., 12.","DOI":"10.1371\/journal.pgen.1006456"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Salazar, J.L., Yang, S.-A., Lin, Y.Q., Li-Kroeger, D., Marcogliese, P.C., Deal, S.L., Neely, G.G., and Yamamoto, S. (2021). Alzheimer\u2019s disease-associated TM2D genes regulate Notch signaling and neuronal function in Drosophila. bioRxiv, 17.","DOI":"10.1101\/2021.04.20.440660"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"18748","DOI":"10.1074\/jbc.M011161200","article-title":"\u03bc-Amyloid peptide-induced apoptosis regulated by a novel protein containing a G protein activation module","volume":"276","author":"Kajkowski","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_33","unstructured":"Neidhardt, F.C. (1996). Escherichia coli and Salmonella: Cellular and Molecular Biology, ASM Press."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1126\/science.284.5416.967","article-title":"An Essential Role for DNA Adenine Methylation in Bacterial Virulence","volume":"284","author":"Heithoff","year":"1999","journal-title":"Science"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"11578","DOI":"10.1073\/pnas.96.20.11578","article-title":"DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity","volume":"96","author":"Pucciarelli","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"7610","DOI":"10.1128\/IAI.69.12.7610-7615.2001","article-title":"DNA adenine methylase is essential for viability and plays a role in the pathogenesis of Yersinia pseudotuberculosis and Vibrio cholerae","volume":"69","author":"Julio","year":"2001","journal-title":"Infect. Immun."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd","volume":"269","author":"Fleischmann","year":"1995","journal-title":"Science"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-59745-522-0_1","article-title":"DNA methylation: An introduction to the biology and the disease-associated changes of a promising biomarker","volume":"507","author":"Tost","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0022-2836(84)90054-8","article-title":"A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome","volume":"177","author":"Lin","year":"1984","journal-title":"J. Mol. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2799","DOI":"10.1128\/jb.175.10.2799-2808.1993","article-title":"Rhs elements of Escherichia coli K-12: Complex composites of shared and unique components that have different evolutionary histories","volume":"175","author":"Zhao","year":"1993","journal-title":"J. Bacteriol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Poole, S.J., Diner, E.J., Aoki, S.K., Braaten, B.A., t\u2019Kint de Roodenbeke, C., Low, D.A., and Hayes, C.S. (2011). Identification of Functional Toxin\/Immunity Genes Linked to Contact-Dependent Growth Inhibition (CDI) and Rearrangement Hotspot (Rhs) Systems. PLOS Genet., 7.","DOI":"10.1371\/journal.pgen.1002217"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4532","DOI":"10.1093\/nar\/gkr036","article-title":"A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems","volume":"39","author":"Zhang","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"7032","DOI":"10.1073\/pnas.1300627110","article-title":"Rhs proteins from diverse bacteria mediate intercellular competition","volume":"110","author":"Koskiniemi","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"4869","DOI":"10.1128\/JB.05061-11","article-title":"Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli","volume":"193","author":"Aggarwal","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Beekman, C., Janson, A.A., Baghat, A., van Deutekom, J.C., and Datson, N.A. (2018). Use of capillary Western immunoassay (Wes) for quantification of dystrophin levels in skeletal muscle of healthy controls and individuals with Becker and Duchenne muscular dystrophy. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0195850"}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/13\/9\/1302\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:33:03Z","timestamp":1760106783000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/13\/9\/1302"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,24]]},"references-count":45,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2024,5]]}},"alternative-id":["foods13091302"],"URL":"https:\/\/doi.org\/10.3390\/foods13091302","relation":{},"ISSN":["2304-8158"],"issn-type":[{"type":"electronic","value":"2304-8158"}],"subject":[],"published":{"date-parts":[[2024,4,24]]}}}