Trypanosomal TBP Functions with the Multisubunit Transcription Factor tSNAP To Direct Spliced-Leader RNA Gene Expression

Das, Apurba K.; Zhang, Qing; Palenchar, Jennifer B.; Chatterjee, Bithi; Cross, George A.M.; Bellofatto, Vivian

doi:10.1128/mcb.25.16.7314-7322.2005

Cited by 72 publications

(77 citation statements)

References 38 publications

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“…Both species appear to encode only one copy of a TBP family protein. Consistent with the modification of their critical Phe residues, TATA-box-containing promoters were not found in either species (Guillebault et al 2002;Ruan et al 2004;Das et al 2005). These findings provide examples in which the TATA-interacting Phe residues had been altered independently of TRF2.…”

Section: Trf2 Evolved Prior To the Emergence Of The Bilateriasupporting

confidence: 66%

TRF2 and the evolution of the bilateria

et al. 2014

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The development of a complex body plan requires a diversity of regulatory networks. Here we consider the concept of TATA-box-binding protein (TBP) family proteins as “system factors” that each supports a distinct set of transcriptional programs. For instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream core promoter element (DPE) motif. These findings led us to investigate the evolution of TRF2. TBP occurs in Archaea and eukaryotes, but TRF2 evolved prior to the emergence of the bilateria and subsequent to the evolutionary split between bilaterians and nonbilaterian animals. Unlike TBP, TRF2 does not bind to the TATA box and could thus function as a new system factor that is largely independent of TBP. We postulate that this TRF2-based system served as the foundation for new transcriptional programs, such as those involved in triploblasty and body plan development, that facilitated the evolution of bilateria.

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Section: Trf2 Evolved Prior To the Emergence Of The Bilateriasupporting

confidence: 66%

TRF2 and the evolution of the bilateria

et al. 2014

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“…In T. brucei this procedure (with modifications in some cases) has been successfully used to analyze the exosome complex (Estevez et al, 2001), to identify members of the RNA editing complex (Panigrahi et al, 2003), to study the composition of RNAP I (Schimanski et al, 2003;Walgraffe et al, 2005;Nguyen et al, 2006) and RNAP II (Devaux et al, 2006;Das et al, 2006) complexes, to determine the composition of U1 small nuclear RNP (Palfi et al, 2005), and to identify proteins involved in synthesis of the spliced-leader RNA (Das et al, 2005;Schimanski et al, 2005). Similarly, in Leishmania tarentolae this protocol has been employed to analyze the editosome complex (Aphasizhev et al, 2003b).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the RNA polymerase II and III complexes in Leishmania major

Martínez‐Calvillo

Saxena

Green

et al. 2007

International Journal for Parasitology

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Transcription of protein-coding genes in Leishmania major and other trypanosomatids differs from that in most eukaryotes and bioinformatic analyses have failed to identify several components of the RNA polymerase (RNAP) complexes. To increase our knowledge about this basic cellular process, we used tandem affinity purification (TAP) to identify subunits of RNAP II and III. Mass spectrometric analysis of the complexes co-purified with TAP-tagged LmRPB2 (encoded by LmjF31.0160) identified seven RNAP II subunits: RPB1, RPB2, RPB3, RPB5, RPB7, RPB10 and RPB11. With the exception of RPB10 and RPB11, and the addition of RPB8, these were also identified using TAP-tagged constructs of one (encoded by LmjF34.0890) of the two LmRPB6 orthologues. The latter experiments also identified the RNAP III subunits RPC1 (C160), RPC2 (C128), RPC3 (C82), RPC4 (C53), RPC5 (C37), RPC6 (C34), RPC9 (C17), RPAC1 (AC40) and RPAC2 (AC19). Significantly, the complexes precipitated by TAP-tagged LmRPB6 did not contain any RNAP I-specific subunits, suggesting that, unlike in other eukaryotes, LmRPB6 is not shared by all three polymerases but is restricted to RNAP II and III, while the LmRPB6z (encoded by LmjF25.0140) isoform is limited to RNAP I. Similarly, we identified peptides from only one (encoded by LmjF18.0780) of the two RPB5 orthologues and one (LmjF13.1120) of the two RPB10 orthologues, suggesting that LmRPB5z (LmjF18.0790) and LmRPB10z (LmjF13.1120) are also restricted to RNAP I. In addition to these RNAP subunits, we also identified a number of other proteins that co-purified with the RNAP II and III complexes, including a potential transcription factor, several histones, an ATPase involved in chromosome segregation, an endonuclease, four helicases, RNA splicing factor PTSR-1, at least two RNA binding proteins and several proteins of unknown function.

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“…The U snRNAs are transcribed in trypanosomes by RNA polymerase III from extragenic tRNA promoters (Nakaar et al 1994). In contrast, the SL RNA is transcribed by an RNA polymerase II-dependent extragenic promoter (Gilinger and Bellofatto 2001;Das et al 2005). Strong evidence was provided for coupling of the unique hypermethylated capping of SL RNA and its transcription (Mair et al 2000).…”

Section: Introductionmentioning

confidence: 98%

Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei

Tkacz

Lustig

Stern

et al. 2006

RNA

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In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we examined the function of these Sm proteins using RNAi silencing and protein purification. RNAi silencing of each of the seven Sm genes resulted in accumulation of SL RNA as well as reduction of several U snRNAs. Interestingly, U2 was unaffected by the loss of SmB, and both U2 and U4 snRNAs were unaffected by the loss of SmD3, suggesting that these snRNAs are not bound by the heptameric Sm complex that binds to U1, U5, and SL RNA. RNAi silencing and protein purification showed that U2 and U4 snRNAs were bound by a unique set of Sm proteins that we termed SSm (specific spliceosomal Sm proteins). This is the first study that identifies specific core Sm proteins that bind only to a subset of spliceosomal snRNAs.

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Trypanosomal TBP Functions with the Multisubunit Transcription Factor tSNAP To Direct Spliced-Leader RNA Gene Expression

Cited by 72 publications

References 38 publications

TRF2 and the evolution of the bilateria

TRF2 and the evolution of the bilateria

Characterization of the RNA polymerase II and III complexes in Leishmania major

Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei

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