title: A strong propensity toward loop formation characterizes the expressed reading frames of the D segments at the Ig H and T cell receptor loci.
abstract: A compilation of murine and human Ig H and TcR beta D segment sequences was used to estimate the relative usage of the various reading frames and to look for associated sequence patterns. We confirm a strong bias in the expression of the Ig H D segments, with more than 90% (murine) and 85% (human) expressed peptides resulting from a preferred reading frame. Remarkably, 86% (mouse) and 90% (human) of those peptides contain at least one glycine residue. All but one of the atypical preferred D peptides contain serine or proline residues and are found in the immediate vicinity of glycine residues provided by specific JH segments. The presence of tyrosine residues is also a characteristic feature of expressed reading frames in both mouse (75%) and human (90%). These results suggest that the constraints of forming a flexible loop within the third complementarity-determining region, is a factor in the preference for a particular reading frame in Ig H D. For the TcR beta D segments, glycine is specified in most reading frames, and no significant preference is observed.
authors.affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
authors.forename: C
authors.initials: C
authors.lastname: Abergel
authors.forename: J M
authors.initials: JM
authors.lastname: Claverie
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000916:Antibody Diversity; D001483:Base Sequence; D003062:Codon; D004247:DNA / Q000235:genetics; D015326:Gene Rearrangement, B-Lymphocyte, Heavy Chain; D015333:Gene Rearrangement, beta-Chain T-Cell Antigen Receptor; D005803:Genes, Immunoglobulin; D005998:Glycine / Q000737:chemistry; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry / Q000235:genetics* / Q000648:ultrastructure; D051379:Mice; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D011487:Protein Conformation; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry / Q000235:genetics* / Q000648:ultrastructure; D012995:Solubility; D014443:Tyrosine / Q000737:chemistry
chemical_list: D003062:Codon; D007143:Immunoglobulin Heavy Chains; D016693:Receptors, Antigen, T-Cell, alpha-beta; D014443:Tyrosine; D004247:DNA; D005998:Glycine