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Mucosal B cells and their function
Published in Phillip D. Smith, Richard S. Blumberg, Thomas T. MacDonald, Principles of Mucosal Immunology, 2020
Jo Spencer, Edward N. Janoff, Per Brandtzaeg
IgA switch factors initiate transcription through switch regions of Cα in cells expressing sIgM. The RNA produced is noncoding and may be referred to as a sterile transcript. Experimentally, the presence of sterile transcripts in a population of B cells reflects the potential for class-switch recombination. The function of sterile germline transcript production is to open up the DNA double helix in a transcription bubble, allowing the molecular mediators of class-switch recombination, including AID, access to single-stranded DNA substrate (see Figure 10.6). The switch regions are long DNA sequences composed largely of repeated nucleotide motifs that include the DNA target substrate for AID. Deamination of cytidine on both DNA strands generates uracil that can be removed by uracil glycosylase. The abasic site can then be recognized by apurinic/apyrimidinic endonuclease that generates nicks in the DNA. The subsequent repair (by a nonhomologous end-joining pathway related to repair of DNA strand breaks during RAG-mediated recombination) replaces the Cμ constant region with Cα, leaving a circular deleted episomal fragment (see Figure 10.6). RNA transcripts of the circular DNA fragment (noncoding circle transcripts) are produced for a short time after the recombination event. Circle transcript production is therefore a feature of class-switch recombination in the recent past history of a B cell—a feature that can be exploited experimentally when investigating class-switch recombination events.
Introduction to Molecular Biology
Published in Martin G. Pomper, Juri G. Gelovani, Benjamin Tsui, Kathleen Gabrielson, Richard Wahl, S. Sam Gambhir, Jeff Bulte, Raymond Gibson, William C. Eckelman, Molecular Imaging in Oncology, 2008
The elongation process is accomplished by base-pairing mechanism as is DNA replication. However, unlike in replication, there is only one transcript and the base pair are RNA-DNA instead of DNA-DNA. While in replication, either DNA strand can serve as a template, in transcription, the polymerase proceeds only along a strand in 3′ to 5′ direction. In other words, the synthesis of the mRNA is 5′ → 3′ directed on the 3′ → 5′ oriented template DNA strand. Thus, the mRNA molecule produced is complementary to the DNA template (3′ → 5′ or antisense) strand and identical to the DNA nontemplate (5′ → 3′ or sense) strand. For the complementary base-pairing process, the same rules are applied, but the AT coupling in DNA-DNA duplex is replaced by an AU coupling in RNA-DNA duplex. The elongation of the RNA chain is catalyzed by the RNA polymerase enzyme, which produces covalent link between each ribonucleoside triphosphate. RNA polymerase contains both unwinding and rewinding activities, so the process forms a structure called transcription bubble that moves along the DNA during the transcription process (Fig. 10).
AID Biology: A pathological and clinical perspective
Published in International Reviews of Immunology, 2018
Meenal Choudhary, Anubhav Tamrakar, Amit Kumar Singh, Monika Jain, Ankit Jaiswal, Prashant Kodgire
The surface of AID is composed of highly positive charged residues which enable its interaction with negatively charged substrate DNA [14]. In contrast to other highly active enzymes, AID has a very slow deamination rate i.e. it catalyzes only a single reaction in several minutes [15]. In addition, AID has a very high binding affinity (nM-range) for the ssDNA substrate and a prolonged half-life of ∼8 min, which gives details about the slow catalytic rate of AID [15]. Biochemical analysis of AID activity suggests that it has high enzymatic processivity as it remains stably bound to ssDNA when the transcription bubble progresses, thereby catalyzing many C->U deamination reactions on the same ssDNA substrate resulting in multiple mutations [14, 16, 17]. Several pieces of evidence suggest that native AID can exist as a monomer, dimer or multimer [18–21]. Nevertheless, studies using atomic force microscopy (AFM) showed that AID in the presence of ssDNA appears to be a monomer [18]. Purified AID migrates as a tetramer [20] whereas co-expression of AID with different tags in the same cell followed by immunoprecipitation of either of the tags yielded both forms, indicating that AID is able to form a multimer [21].