title: The PII superfamily revised: a novel group and evolutionary insights.
abstract: The PII proteins compose a superfamily of signal transducers with fundamental roles in the nitrogen metabolism of prokaryotic organisms. They act at different cellular targets, such as ammonia transporters, enzymes, and transcriptional factors. These proteins are small, highly conserved, and well distributed among prokaryotes. The current PII classification is based on sequence similarity and genetic linkage. Our work reviewed this classification through an extensive analysis of PII homologues deposited in GenBank. We also investigated evolutionary aspects of this ancient protein superfamily and revised its PROSITE signatures. A new group of PII proteins is described in this work. These PII homologues have a peculiar genetic context, as they are associated with metal transporters and do not contain the canonical PROSITE signatures of PII. Our analysis reveals that horizontal gene transfer could have played an important role in PII evolution. Thus, new insights into PII evolution, a new PII group, and more comprehensive PROSITE signatures are proposed.
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Fernando Hayashi
authors.initials: FH
authors.lastname: Sant'Anna
authors.forename: Débora Broch
authors.initials: DB
authors.lastname: Trentini
authors.forename: Shana
authors.initials: S
authors.lastname: de Souto Weber
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cecagno
authors.forename: Sérgio Ceroni
authors.initials: SC
authors.lastname: da Silva
authors.forename: Irene Silveira
authors.initials: IS
authors.lastname: Schrank
mesh_terms: D000595:Amino Acid Sequence; D015806:Azospirillum brasilense / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D051922:PII Nitrogen Regulatory Proteins / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D051922:PII Nitrogen Regulatory Proteins; D012336:RNA, Ribosomal, 16S; C084296:nifL protein, Bacteria