title: A systematic survey of mini-proteins in bacteria and archaea.
abstract: BACKGROUND
  Mini-proteins, defined as polypeptides containing no more than 100 amino acids, are ubiquitous in prokaryotes and eukaryotes. They play significant roles in various biological processes, and their regulatory functions gradually attract the attentions of scientists. However, the functions of the majority of mini-proteins are still largely unknown due to the constraints of experimental methods and bioinformatic analysis.
  
  
  RESULTS
  In this article, we extracted a total of 180,879 mini-proteins from the annotations of 532 sequenced genomes, including 491 strains of Bacteria and 41 strains of Archaea. The average proportion of mini-proteins among all genomic proteins is approximately 10.99%, but different strains exhibit remarkable fluctuations. These mini-proteins display two notable characteristics. First, the majority are species-specific proteins with an average proportion of 58.79% among six representative phyla. Second, an even larger proportion (70.03% among all strains) is hypothetical proteins. However, a fraction of highly conserved hypothetical proteins potentially play crucial roles in organisms. Among mini-proteins with known functions, it seems that regulatory and metabolic proteins are more abundant than essential structural proteins. Furthermore, domains in mini-proteins seem to have greater distributions in Bacteria than Eukarya. Analysis of the evolutionary progression of these domains reveals that they have diverged to new patterns from a single ancestor.
  
  
  CONCLUSIONS
  Mini-proteins are ubiquitous in bacterial and archaeal species and play significant roles in various functions. The number of mini-proteins in each genome displays remarkable fluctuation, likely resulting from the differential selective pressures that reflect the respective life-styles of the organisms. The answers to many questions surrounding mini-proteins remain elusive and need to be resolved experimentally.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Fengyu
authors.initials: F
authors.lastname: Wang
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.forename: Linlin
authors.initials: L
authors.lastname: Pan
authors.forename: Ming
authors.initials: M
authors.lastname: Yang
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Zhang
authors.forename: Shouguang
authors.initials: S
authors.lastname: Jin
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001105:Archaea / Q000378:metabolism*; D019843:Archaeal Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D008954:Models, Biological; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins