title: Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus.
abstract: Genetic studies in Lotus japonicus and pea have identified Nin as a core symbiotic gene required for establishing symbiosis between legumes and nitrogen fixing bacteria collectively called Rhizobium. Sequencing of additional Lotus cDNAs combined with analysis of genome sequences from Arabidopsis and rice reveals that Nin homologues in all three species constitute small gene families. In total, the Arabidopsis and rice genomes encode nine and three NIN-like proteins (NLPs), respectively. We present here a bioinformatics analysis and prediction of NLP evolution. On a genome scale we show that in Arabidopsis, this family has evolved through segmental duplication rather than through tandem amplification. Alignment of all predicted NLP protein sequences shows a composition with six conserved modules. In addition, Lotus and pea NLPs contain segments that might characterize NIN proteins of legumes and be of importance for their function in symbiosis. The most conserved region in NLPs, the RWP-RK domain, has secondary structure predictions consistent with DNA binding properties. This motif is shared by several other small proteins in both Arabidopsis and rice. In rice, the RWP-RK domain sequences have diversified significantly more than in Arabidopsis. Database searches reveal that, apart from its presence in Arabidopsis and rice, the motif is also found in the algae Chlamydomonas and in the slime mold Dictyostelium discoideum. Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide.
authors.affiliation: Laboratory of Gene Expression, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Arhus C, Denmark. schauser@daimi.au.dk
authors.forename: Leif
authors.initials: L
authors.lastname: Schauser
authors.forename: Wioletta
authors.initials: W
authors.lastname: Wieloch
authors.forename: Jens
authors.initials: J
authors.lastname: Stougaard
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D000070116:Lotus / Q000235:genetics* / Q000382:microbiology; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013559:Symbiosis / Q000235:genetics; D013997:Time Factors
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; C403406:NIN protein, Lotus japonicus; D010940:Plant Proteins