{
  "abstract": "Hypothetical proteins (HPs), known as biological dark matter, are genetic sequences of which the biological functions and regulatory processes remain largely unclear. In Pseudomonas aeruginosa, HPs account for 36.4% of all coding genes, representing a significant gap in understanding their functions and contribution to the virulence network. To address these challenges, we present a deletion repertoire comprising 938 strains targeting 1165 HPs in P. aeruginosa. Starting with transcriptome-wide analysis, we inferred putative functional predictions for HP mutants through systematic profiling of differential expression and candidate transcriptional pathways. We integrated our expression profiles with public datasets (5707 genes × 2312 conditions). This allowed us to distinguish constitutively expressed genes from variable genes. Using independent component analysis (ICA), we identified 56 independent regulatory Modules, providing a comprehensive transcriptional-association framework. These contributed to the discovery and experimental validation of 20 virulence-related hypothetical proteins (VRHPs) and 3 antibiotic resistance-related hypothetical proteins (ARHPs). Evolutionary analysis across bacterial taxa provided additional insights into HP sequence conservation and evolutionary dynamics. In summary, our study presents a large-scale HP mutant library combined with integrated transcriptomic and machine learning approaches, establishing both a valuable resource and a systematic strategy for predicting and prioritizing candidate functions of HPs across bacterial species.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Agricultural and Forestry Biosecurity, The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China.",
    "Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree, Guangzhou, China.",
    "Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.",
    "College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.",
    "School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.",
    "State Key Laboratory of Agricultural and Forestry Biosecurity, The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China. xlshao@njau.edu.cn.",
    "Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China. xlshao@njau.edu.cn.",
    "Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China. xindeng@cityu.edu.hk.",
    "Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong, China. xindeng@cityu.edu.hk."
  ],
  "article_type": "research support, non u.s. gov't",
  "arxiv": null,
  "author_total": 18,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Chunyan Yao"
    },
    {
      "affs": [
        2
      ],
      "name": "Beifang Lu",
      "orcid": "0009-0000-8070-8567"
    },
    {
      "affs": [
        1
      ],
      "name": "Yiqing Ding"
    },
    {
      "affs": [
        2
      ],
      "name": "Letong Xu",
      "orcid": "0009-0001-8897-0591"
    },
    {
      "affs": [
        3
      ],
      "name": "Jingui Liu"
    },
    {
      "affs": [
        2
      ],
      "name": "Yingchao Zhang"
    },
    {
      "affs": [
        2
      ],
      "name": "Jiadai Huang",
      "orcid": "0000-0002-4104-6836"
    },
    {
      "affs": [
        2
      ],
      "name": "Yue Sun",
      "orcid": "0009-0008-2843-0017"
    },
    {
      "affs": [
        2
      ],
      "name": "Na Liu"
    },
    {
      "affs": [
        2
      ],
      "name": "Fang Chen",
      "orcid": "0000-0002-2154-4440"
    },
    {
      "affs": [
        2
      ],
      "name": "Shumin Li"
    },
    {
      "affs": [
        2
      ],
      "name": "Tianmin Li",
      "orcid": "0000-0001-9811-8549"
    },
    {
      "affs": [
        2
      ],
      "name": "Tongtong Feng",
      "orcid": "0009-0000-0362-1345"
    },
    {
      "affs": [
        2
      ],
      "name": "Youyue Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Guoliang Qian",
      "orcid": "0000-0003-3577-3241"
    },
    {
      "affs": [
        4
      ],
      "name": "Aixin Yan",
      "orcid": "0000-0003-0310-5492"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Xiaolong Shao",
      "orcid": "0000-0002-7425-2249"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Xin Deng",
      "orcid": "0000-0003-1580-0089"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2x1tz3c29t83z.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-77512-1",
  "fulltext_url": "https://europepmc.org/articles/PMC13680508",
  "id": "2x1tz3c29t83z",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://europepmc.org/article/MED/42897133",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1311|Bacterial Genetics and Biotechnology"
    ]
  ],
  "openalex": "W7213457205",
  "pdf_url": "https://europepmc.org/articles/PMC13680508?pdf=render",
  "pmcid": "PMC13680508",
  "pmid": "42897133",
  "published": "2026-09-17",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/2x1tz3c29t83z.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:41Z",
      "native_id": "MED:42897133",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42897133"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Bacterial Genetics and Biotechnology",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Characterization of hypothetical proteins reveals function modules and virulence factors in Pseudomonas aeruginosa.",
  "title_text": "Characterization of hypothetical proteins reveals function modules and virulence factors in Pseudomonas aeruginosa.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:41Z",
  "url": "https://research.draconitic.com/paper/2x1tz3c29t83z",
  "venue": "Nature communications",
  "versions": []
}