TAL Gene Family (SCL)

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TA L G e ne F a m i l y (SCL)

bases, which are bracketed by a direct repeat of 5 nt pairs, appear to be pushed out in a kind of hairpin loop so that the codons on either side of it are brought together. Though the structure at this point is unusual, a ribosome can presumably move right through it, translating the messenger properly while ignoring all the nucleotides in the loop. This segment of gene 60 was inserted into the N-terminal coding sequence of the b-galactosidase gene of E. coli, where it also was neither excised nor translated. The fused genes showed comparable levels of enzyme activity to a fusion without the extra 50 bases, indicating that the looped-out sequence has little effect on translation of the messenger. This ribosomal bypass region has been found only in gene 60 of T4 and a few of the other T-even phages; there is nothing like it in the comparable gene of phages T2, T6, and most other family members. In those cases, T4's gene 60 is actually fused with the gene for another topoisomerase subunit, coded in T4 by gp39. In T4, genes 39 and 60 are separated by several hundred base pairs that are noncoding except for what appears to be the residue of one of the homing endonuclease genes described here.

Conclusions Bacteriophages, especially the large, complex phages discussed here, have long been a major focus of molecular biology. An amazing amount of basic biological information has been uncovered with the T-even coliphages alone. Although much of the excitement of molecular biology has now shifted to eukaryotic systems, many investigators continue to work with phages and continue to astonish their colleagues with discoveries of previously undreamt-of mechanisms and processes. Phage systems, which are relatively easy to handle and involve inexpensive materials and short time scales, remain excellent material for working out the details of many kinds of complex mechanisms and for training young investigators. One major advantage is the degree of genetic understanding of the phage-host system and the ability to combine genetic, physical, and biochemical tools in attacking a problem. But this line of work reemphasizes an important point about biological research: that simply knowing the structure of a DNA molecule is not enough, because the sequence of nucleotides tells little about the function of that sequence, even though it may yield important clues. Biology is something more than chemistry. A gene is not merely a segment of a DNA molecule; it is a meaningful segment, which must be expressed and regulated, often through complex mechanisms, and there is no way to know those mechanisms a priori just by doing chemical

experiments. This has again been reemphasized with the discovery of the folded-out intron in gene 60. Molecular biology has been fruitful primarily because it combines chemical work with biological ± especially genetic ± studies. And much of its fascination lies in its promise of another surprise after every experiment.

Further Reading

Karam J et al. (eds) (1994) Molecular Biology of Bacteriophage T4. Webster R and Granoff A (eds) (1994) Encyclopedia of Virology. London: Academic Press

References

Ackermann and Krisch (1997) Archives of Virology 142: 2329± 2345. Benzer S (1955) Fine structure of a genetic region in bacteriophage. Proceedings of the National Academy of Sciences, USA 41: 344±354. Chu FK, Maley GF, Maley F et al. (1984) Intervening sequence is the thymidylats synthesis gene of bacteriophage T4. Proceedings of the National Academy of Sciences, USA. 1(10): 3049±3053. Demerec M and Fano U (1945) Bacteriophage-resistant mutants in Escherichia coli. Genetics 30: 119±136. Ellis EL and DelbruÈck M (1939) The growth of bacteriophage. Journal of General Physiology 22: 365±384. Epstein RH, Bolle A and Steinberg C et al. (1963) Physiological studies of conditional lethal mutants of bacteriophage T4D. Cold Spring Harbor Symposia on Quantitative Biology 28: 375±392. Hershey AD and Chase M (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. Journal of General Physiology 36: 39 ± 56. Hershey AD and Rotman R (1948) Linkage among genes controlling inhibition of lysis in a bacterial virus. Proceedings of the National Academy of Sciences, USA 34: 89±96. Huang WM, Ao S-Z, Casjens S et al. (1988) A persistent untranslated sequence within T4 DNA topoisomerase gene 60. Science 239: 1005±1012. Kutter E, Gachechiladze K, Poglazov A et al. (1996) Evolution of T4-Related Phages. Virus Genes 11: 285±297.

See also: Bacteriophages; Lysogeny

TAL Gene Family (SCL) R Baer Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1625

The TAL family consists of three proto-oncogenes (TAL1, TAL2, and LYL1) that were identified through

TAL G e n e F a m i l y ( S C L) 1931 the analysis of tumor-specific chromosomal translocations associated with human T-cell acute lymphoblastic leukemia (T-ALL). Each of these genes encodes a polypeptide that harbors the basic helix±loop±helix domain (bHLH), a DNA-binding motif common to many eukaryotic transcription factors. Since the bHLH domains of TAL1, TAL2, and LYL1 are more closely related to one another than to those of other proteins, they constitute a discrete subgroup within the larger family of bHLH proteins (Figure 1). Nevertheless, each of the TAL genes has a different pattern of tissue-specific expression during normal development. Also, while gene targeting has shown that the mouse Tal1 protein (also called Scl) is essential for the formation of all blood cell lineages, similar studies have not revealed overt defects of hemapoiesis in mice devoid of Tal2 or Lyl1. Thus, despite their common role in leukemogenesis and the striking amino acid sequence homology of their respective bHLH domains, it appears that each of the TAL genes has assumed distinct functions during mammalian development.

of two separate polypeptides can interact to form a dimer that binds DNA as a parallel, left-handed fourhelix bundle. Sequence-specific DNA recognition is mediated primarily by a stretch of basic amino acids that reside near the N-terminal flank of each dimerized bHLH motif (Figure 1). Although some bHLH proteins can form homodimers, the TAL proteins only bind DNA upon heterodimerization with the `E proteins,' a distinct subgroup of bHLH proteins encoded by the E2A, E2-2, and HEB genes. These heterodimers (e.g., TAL1/E2A) have been shown to bind DNA in a sequence-specific fashion and to modulate the transcription of reporter genes that contain a cognate recognition sequence. Thus, at the biochemical level, the TAL proteins appear to function as transcription factors. The bHLH domains of TAL1, TAL2, and LYL1 also interact with the LIM domains of the LIM-only oncoproteins LMO1 and LMO2. This interaction allows for the assembly of a larger DNA-binding complex, which includes not only a bHLH heterodimer such as TAL1/E2A but also a member of the GATA transcription factor family. One such oligomeric complex (E2A/TAL1/LMO2/LBD/GATA-1) has been observed in erythroid cells as well as in leukemic T cells derived from patients with T-ALL. This complex binds DNA in a bidentate fashion in which the E2A/TAL1 heterodimer contacts its recognition sequence on DNA (the E-box), while

TAL Proteins Serve as DNA-Binding Transcription Factors The bHLH motif is a structural domain of 50±60 amino acids that forms two amphipathic a-helices separated by an intervening loop (Figure 1). The bHLH domains (A)

bHLH TAL1

--- COOH 331 bHLH

TAL2

--- COOH 108 bHLH --- COOH

LYL1

267

(B) Basic region

α−Helix 1

α−Helix 2

RRIFTNSRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLL + ++++ ++++++++++ +++ ++++++++++++++++++ +++++ +++++ + + TAL2 RKIFTNTRERWRQQNVNSAFAKLRKLIPTHPPDKKLSKNETLRLAMRYINFLVKVL + +++ ++++++++++ +++ ++++ ++++++ ++++++ +++++ ++ +++ + LYL1 RRVFTNSRERWRQQNVNGAFAELRKLLPTHPPDRKLSKNEVLRLAMKYIGFLVRLL + + ++ + + ++ + + + + + ++ MYC KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEE TAL1

Figure 1 TAL family of basic helix±loop±helix (bHLH) proteins. (A) Schematic of the TAL1, TAL2, and LYL1 gene products. Shaded bars represent the DNA-binding bHLH domains. (B) An alignment of amino acid sequences from the bHLH domains. Whereas the bHLH motifs of TAL1, TAL2, and LYL1 share more than 85% amino acid identity, they are less similar to the corresponding motifs of other bHLH proteins (e.g., MYC).

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Tan d e m R ep e a t s

GATA-1 binds a neighboring GATA sequence (see Figure 1 in LMO Family of LIM-only Genes).

might impair T-cell maturation and thereby increase the likelihood of leukemic transformation.

Role of TAL Genes in T-Cell Leukemia

Further Reading

Certain lymphoid malignancies are characterized by common chromosome abnormalities that can be found in almost all affected patients. For example, more than 95% of patients with Burkitt's lymphoma have chromosome translocations that activate the MYC proto-oncogene, while most cases of follicular B-cell lymphoma feature a translocation that activates the BCL2 proto-oncogene. In contrast, cytogenetic studies have not uncovered a common chromosomal defect associated with T-ALL. Instead, a series of rare, but recurrent, chromosome translocations are found in T-ALL patients. Each results in the transposition of a proto-oncogene into the T-cell receptor (TCR) locus on either chromosome 7 (TCR b-chain) or 14 (TCR a/d-chain). Of the nine proto-oncogenes known to be activated in this manner in T-ALL, three encode the members of the TAL family and two encode the LIM-only proteins with which they are known to interact (i.e., LMO1 and LMO2). Thus, although the chromosomal abnormalities associated with T-ALL are diverse, many of them target proteins within the same biochemical pathway. Moreover, malignant activation of the TAL1 gene is especially frequent in T-ALL. While chromosomal translocations involving TAL1 are observed in only 3% of cases, an additional 25% of patients harbor local rearrangements of the TAL1 gene and nearly half of all pediatric cases show evidence of tumor-specific TAL1 activation. As such, TAL1 represents the most commonly activated proto-oncogene known to be involved in T-ALL. TAL1, TAL2, and LYL1 are not expressed during T-cell development. In contrast, the translocated alleles of these genes are actively transcribed in TALL cells, suggesting that ectopic expression of any one of these genes in the T-cell lineage is potentially leukemogenic. This has been confirmed using mouse models in which targeted expression of a Tal1 transgene in thymocytes results in the formation of clonal T-cell leukemias after a long latency. The exact mechanisms by which ectopic expression of the TAL genes elicits T-cell tumorigenesis are not clear. DNAbinding protein complexes containing, for example, TAL1 might promote leukemogenesis by altering the normal pattern of gene expression in T-lineage cells. Alternatively, the TAL gene products might serve as dominant-negative inhibitors of the E proteins, which normally function as homodimeric bHLH transcription factors during lymphoid development. By disrupting these E-protein homodimers, ectopic TAL1

Baer R, Hwang LY and Bash RO (1997) Transcription factors of the bHLH and LIM families: synergistic mediators of T cell acute leukemia? Current Topics in Microbiology and Immunology 220: 55±65. Rabbitts TH (1998) LMO T-cell translocation oncogenes typify genes activated by chromosomal translocations that alter transcription and developmental processes. Genes and Development 12: 2651±2657.

See also: Leukemia, Acute; LMO Family of LIM-only Genes; Oncogenes; Transcription; Translocation

Tandem Repeats S T Lovett Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1269

Repeated DNA segments are sometimes found adjacent to each other in a direct orientation. Schematically, if `ABCD' represents an ordered genetic sequence, a direct tandem repeat could consist of `ABCBCD,' with segment `BC' being the repeat unit. Such tandem repeats can be of various lengths ranging from several nucleotides to entire groups of genes. Tandem repeats can occur both in coding and noncoding DNA sequences. In certain instances, large numbers of these DNA repeats can found in direct orientation in repeat arrays. For example, the nucleolar organizer region of many organisms including Xenopus, Drosophila, and humans carries hundreds of rRNA genes in a tandem repeat array. One prominent characteristic of tandem repeats is their instability. Tandem repeats are prone to both increases (such as `ABCBCD' to `ABCBCBCD') and decreases (`ABCBCD' to `ABCD') in the number of repeat elements. Such rearrangements are believed to occur by homologous recombination between the repeated DNA segments (including unequal crossingover between chromosomes) or by slipped misalignment of the repeat sequences during DNA replication. Repeats at a variety of genetic loci in humans are variable enough among individuals (so-called variable number tandem repeats or VNTR) that they have been used as molecular `fingerprints' for forensic purposes. For certain loci in humans, rearrangements between tandem repeats can lead to genetic disease. For example, in Huntington disease, fragile X syndrome, or