Terminal deoxynucleotidyltransferase containing megadalton complex from young rat thymus nuclei: identification and characterization

Pandey, Virendra N.; Davé, Vibhuti P.; Patil, M. S.; Pradhan, D.S.; Amrute, Sheela; Modak, Mukund J.

doi:10.1021/bi00469a002

Cited by 13 publications

(16 citation statements)

References 21 publications

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“…TdT activity affects the coding-end sequences by catalyzing the addition of nontemplated nucleotides, which may positively or negatively affect the pairing of coding ends. TdT is also associated with a 5Ј-3Ј exonuclease activity (24). Interaction of these activities will generate coding ends terminating in various configurations.…”

Section: Discussionmentioning

confidence: 99%

The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences

Ezekiel

Sun

Bozek

et al. 1997

Molecular and Cellular Biology

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V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding-and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5 of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the templatedependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.Immunoglobulin (Ig) and T-cell receptor (TCR) genes are expressed in B and T lymphocytes, where they encode antibody and TCR molecules, respectively. Early in lymphocyte development, at the pre-B-and pre-T-cell stages, functional Ig and TCR genes are produced by the rearrangement of V, D, and J gene segments (19). The gene segments are flanked by recombination signal sequences (RSSs) that are composed of 7 and 9 conserved nucleotides separated by nonconserved 12-or 23-nucleotide spacers. During V(D)J recombination, a doublestrand cleavage occurs at the border of the signal and the coding ends. The signal ends join, forming a perfect signal joint, and the coding ends join, creating an imperfect coding joint. The imprecision in the coding junctions creates further diversity in the Ig and TCR genes. Imprecision at the coding ends is due to deletion and/or insertion of nucleotides. Two types of sequence insertions occur at the coding joint. The first, N nucleotide addition, is due to the action of terminal deoxynucleotidyl transferase (TdT), which adds nontemplated nucleotides. The second, P (for palindromic) insertion, denotes the presence of short inverted-repeat sequences adjacent to the nontruncated V, D, or J gene segments.V(D)J recombination can be divided into two phases: cleavage at the RSSs, followed by processing of the signal and coding ends into signal and coding joints. If the process is impaired at the cleavage step, neither signal nor coding joints are formed. If cleavage occurs but processing is completely inhibited...

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Section: Discussionmentioning

confidence: 99%

The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences

Ezekiel

Sun

Bozek

et al. 1997

Molecular and Cellular Biology

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“…In particular, near the bilayer center significant electrostatic interactions are difficult to break without a catalyst (101). This is the primary reason why helices are formed in the headgroup region and then inserted across the membrane (78); the polypeptide has little chance of recouping from any nonnative hydrogen bonds formed in the hydrophobic core of the membrane. In addition, across membranes the water concentration varies over many orders of magnitude, with an especially large gradient when significant concentrations of cholesterol, sphingomyelin, and methylated acyl chains are present (26, 62, 86).…”

Section: Membrane Proteins and Their Membrane Environmentsmentioning

confidence: 99%

Influences of Membrane Mimetic Environments on Membrane Protein Structures

Zhou

Cross

2013

Annu. Rev. Biophys.

240

302

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The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins.

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“…However, the precise temporal relationship between TdT gene expression and T cell receptor gene rearrangement during in vivo mature T cell development in the thymus is still unknown. Although TdTshows ill vitro DNA polymerization activity as a 58 kDa monomer, it has been speculated that the N region is synthesized by the orchestration of many proteins, including TdT (32). In particular, the biochemical mechanisms able to activate and inactivate the function ofTdT ill vivo are not yet fully elucidated.…”

Section: /N Vivo Phosphorylation Assay Tdtwas Recovered By Immunoprmentioning

confidence: 99%

Involvement of Caspase-3 in the Cleavage of Terminal Transferase

Trubiani

Guarnieri

Paganelli

et al. 2002

Int J Immunopathol Pharmacol

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To investigate the ill vivo role of caspase-3 in Terminal Transferase metabolism DMSO-treated RPMI-8402, a human pre-T cell line was used. In DMSO treated samples 3H·dGTP incorporation and TdT phosphorylation occurs after 4 hours of treatment. After 8 hours cells undergo TdT proteolysis in addition to its inactivation. The cleavage ofTdT into 32· and 58-KDa proteolytic fragments occurred simultaneously with the activation of Caspase-3, but preceded changes associated with the apoptotic process described after 48 hours of treatment. The Caspase-3 peptide inhibitor V, used as a specific inhibitor, prevented TdT proteolysis prolonging its activity and rescued cells from apoptosis. Our experiments suggest that TdT is a nuclear substrate for Caspase-3, the main apoptotic effector protease in many cell types, and that the cleavage of TdT represents a primary step in a signal cascade leading to pre-T cell apoptosis.

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Terminal deoxynucleotidyltransferase containing megadalton complex from young rat thymus nuclei: identification and characterization

Cited by 13 publications

References 21 publications

The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences

The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences

Influences of Membrane Mimetic Environments on Membrane Protein Structures

Involvement of Caspase-3 in the Cleavage of Terminal Transferase

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