Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.Choanoflagellates have long fascinated evolutionary biologists for their marked similarity to the 'feeding cells' (choanocytes) of sponges and the possibility that they might represent the closest living relatives of metazoans 1,2 . Over the past decade or so, evidence supporting this relationship has accumulated from phylogenetic analyses of nuclear and mitochondrial genes [3][4][5][6] , comparative genomics between the mitochondrial genomes of choanoflagellates, sponges and other metazoans 7,8 , and the finding that choanoflagellates express homologues of metazoan signalling and adhesion genes 9-12 . Furthermore, species-rich phylogenetic analyses demonstrate that choanoflagellates are not derived from metazoans, but instead represent a distinct lineage that evolved before the origin and diversification of metazoans (Fig. 1a, Supplementary Fig. 1 and Supplementary Note 3.1) 8,13 . By virtue of their position on the tree of life, studies of choanoflagellates provide an unparallelled window into the nature of the unicellular and colonial progenitors of metazoans 14 .Choanoflagellates are abundant and globally distributed microbial eukaryotes found in marine and freshwater environments 15,16 . Like sponge choanocytes, each cell bears an apical flagellum surrounded by a distinctive collar of actin-filled microvilli, with which choanoflagellates trap bacteria and detritus (Fig. 1b). Using this highly effective means of prey capture, choanoflagellates link bacteria to higher trophic levels and thus have critical roles in oceanic carbon cycling and in the microbial food web 17,18 .More than 125 choanoflagellate species have been identified, and all species have a unicellular life-history stage. Some can also form simple colonies of equipotent cells, although these differ substantially from the obligate associations of differentiated cells in metazoans 19 . Studies of basal metazoans indicate that the ancestral metazoan was multicellular and had differentiated cell types, an epithelium, a body plan and regulated development including gastrulation. In contrast, the last common ancestor of choanoflagellates and metazoans was unicellular or possibly capable of forming simple colonies, underscoring the abundant biologi...

The Drosophila insulin receptor (dInR) regulates cell growth and proliferation through the dPI3K/dAkt pathway, which is conserved in metazoan organisms. Here we report the identification and functional characterization of the Drosophila forkhead-related transcription factor dFOXO, a key component of the insulin signaling cascade. dFOXO is phosphorylated by dAkt upon insulin treatment, leading to cytoplasmic retention and inhibition of its transcriptional activity. Mutant dFOXO lacking dAkt phosphorylation sites no longer responds to insulin inhibition, remains in the nucleus, and is constitutively active. dFOXO activation in S2 cells induces growth arrest and activates two key players of the dInR/dPI3K/dAkt pathway: the translational regulator d4EBP and the dInR itself. Induction of d4EBP likely leads to growth inhibition by dFOXO, whereas activation of dInR provides a novel transcriptionally induced feedback control mechanism. Targeted expression of dFOXO in fly tissues regulates organ size by specifying cell number with no effect on cell size. Our results establish dFOXO as a key transcriptional regulator of the insulin pathway that modulates growth and proliferation. During the development of multicellular organisms, growth is tightly regulated by controlling cell number and cell size so that each organ reaches its appropriate dimensions in relation to the size of the organism. Many studies indicate that growth and proliferation are coordinated but distinct processes and that cells progress through the cell cycle only when sufficient mass, size, and macromolecular biosynthesis have been reached. (Hartwell et al. 1974;Johnston et al. 1977;Weigmann et al. 1997). Organism growth is controlled by coordinating both cell cycle progression and survival, which is modulated by nutrient availability, growth factors, and temperature. Growth factors can stimulate cell division and survival by activating the insulin receptor, which in turn acts through two main signal transduction cascades: the Ras/MAP kinase (Lee and McCubrey 2002) and the PI3K/ Akt kinase pathways (Cantley 2002). Insulin-mediated activation of PI3K increases production of 3Ј-phosphorylated phosphoinositide lipids (PIP 3 ) that serve as second messengers to recruit Akt to the plasma membrane (Datta et al. 1999). Once properly localized in the membrane, Akt becomes activated by phosphorylation and in turn phosphorylates a number of downstream targets that ultimately regulate cell growth. For example, Akt stimulates protein synthesis through activation of the target of rapamycin (TOR) kinase, which subsequently phosphorylates and inactivates the translational repressor eukaryotic initiation factor 4E-binding protein (4EBP; Gingras et al. 2001).In addition to modulating translation, Akt regulates transcription through the forkhead-related FOXO family of transcription factors FOXO1, FOXO3a, and FOXO4 (Burgering and Kops 2002) by phosphorylating these proteins at three conserved serine/threonine residues. This leads to retention of FOXO transcription factor...

Transcription and DNA repair are coupled in E. coli by the Mfd protein, which dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. We show that Mfd influences the elongation state of RNA polymerase (RNAP); transcription complexes that have reverse translocated into the backtracked position, a potentially important intermediate in RNA proofreading and repair, are restored to the forward position by the activity of Mfd, and arrested complexes are rescued into productive elongation. Mfd may act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNA polymerase when the enzyme active site cannot continue elongation.

To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. Eighty-seven percent of the introns assayed manifest >50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly or slowly, with~3% being almost completely retained in nascent pre-mRNA. Although individual introns showed slight but statistically significant differences in splicing efficiency, similar global levels of splicing were seen from both sources. Importantly, introns with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific. The analysis also indicates that cotranscriptional splicing is less efficient for first introns, longer introns, and introns annotated as alternative. Finally, S2 cells expressing the slow RpII215 C4 mutant show substantially less intron retention than wild-type S2 cells.

In transcription initiation, the DNA strands must be separated to expose the template to RNA polymerase. As the closed initiation complex is converted to an open one, specific protein-DNA interactions involving bases of the nontemplate strand form and stabilize the promoter complex in the region of unwinding. Specific interaction between RNA polymerase and the promoter in Escherichia coli was detected and quantified as the binding affinity of nontemplate oligonucleotide sequences. The RNA polymerase subunit sigma factor 70 contacted the bases of the nontemplate DNA strand through its conserved region 2; a mutation that affected promoter function altered the binding affinity of the oligonucleotide to the enzyme.

Nudler et al., 1997), in which RNAP has backtracked, or moved upstream relative to the DNA, displacing the 3Ј end of the transcript from Summary the active site (Figure 1). Eukaryotic and archael RNAP carry out identical reactions (Izban and Luse, 1992; Gre proteins of prokaryotes, and SII proteins of eu-Hausner et al., 2000). Backtracking of artificially stalled and karyotes and archaea, are transcription elongation paused enzymes is well documented in vitro, especially for factors that promote an endogenous transcript cleav-E. coli RNAP, but has not been observed in vivo. age activity of RNA polymerases; this process pro-Since the progress of transcription is important to motes elongation through obstructive regions of DNA, gene expression, it is not surprising that the cell contains including transcription pauses that act as sites of gefactors to mediate the cleavage of RNA in backtracked netic regulation. We show that a regulatory pause in complexes. GreA and GreB in E. coli, and TFIIS (SII) in the early part of the late gene operon of bacteriophage eukaryotes and archaea, are transcription elongation is subject to such cleavage and resynthesis. In cells factors that induce cleavage of backtracked complexes lacking the cleavage factors GreA and GreB, the pause in vitro and are presumed to do so in vivo (Reines et is prolonged, and RNA polymerase occupies a variant al., 1989; Borukhov et al., 1992, 1993; Borukhov and position at the pause site. Furthermore, GreA and GreB Goldfarb, 1996; Hausner et al., 2000). The greA gene was are required to mediate efficient function of the gene identified originally as a suppressor of a temperature-Q antiterminator at this site. Thus, cleavage factors sensitive RNA polymerase core (rpoB) mutation, thereby are necessary for the natural progression of RNA polyestablishing its function in transcription (Sparkowski merase in vivo. and Das, 1990). Biochemical experiments showed that GreA and GreB act by stimulating an internal hydrolytic

Activator-dependent recruitment of TFIID initiates formation of the transcriptional preinitiation complex. TFIID binds core promoter DNA elements and directs the assembly of other general transcription factors, leading to binding of RNA polymerase II and activation of RNA synthesis. How TATA box-binding protein (TBP) and the TBP-associated factors (TAFs) are assembled into a functional TFIID complex with promoter recognition and coactivator activities in vivo remains unknown. Here, we use RNAi to knock down specific TFIID subunits in Drosophila tissue culture cells to determine which subunits are most critical for maintaining stability of TFIID in vivo. Contrary to expectations, we find that TAF4 rather than TBP or TAF1 plays the most critical role in maintaining stability of the complex. Our analysis also indicates that TAF5, TAF6, TAF9, and TAF12 play key roles in stability of the complex, whereas TBP, TAF1, TAF2, and TAF11 contribute very little to complex stability. Based on our results, we propose that holo-TFIID comprises a stable core subcomplex containing TAF4, TAF5, TAF6, TAF9, and TAF12 decorated with peripheral subunits TAF1, TAF2, TAF11, and TBP. Our initial functional studies indicate a specific and significant role for TAF1 and TAF4 in mediating transcription from a TATA-less, downstream core promoter element (DPE)-containing promoter, whereas a TATA-containing, DPE-less promoter was far less dependent on these subunits. In contrast to both TAF1 and TAF4, RNAi knockdown of TAF5 had little effect on transcription from either class of promoter. These studies significantly alter previous models for the assembly, structure, and function of TFIID.RNA interference ͉ TATA box-binding protein ͉ S2 cells R egulated initiation of transcription to produce mRNA in eukaryotes requires the stepwise assembly of an elaborate multiprotein preinitiation complex consisting of the general transcription factors, various coactivators, and RNA polymerase II (for review, see ref. 1). The core promoter-recognition complex, TFIID, consists of the TATA box-binding protein (TBP) and 8-12 TBP-associated factors (TAFs). In addition to binding core promoter elements and initiating formation of the preinitiation complex, this TBP⅐TAF multisubunit transcription factor also serves as a coactivator by transmitting signals from sequence-specific activators to other components of the basal machinery (for review, see ref.2).Critical to dissecting the diverse functions of TFIID in both promoter recognition and coactivation is an understanding of how the complex is assembled and maintained in cells. Initial in vitro assembly reactions suggested that TBP and the largest TAF subunit (TAF1) may form a scaffold on which the other TAFs bind to form holo-TFIID (3). Subsequent studies have proposed that TAF5 may dimerize and also help coordinate complex assembly (4). Recent low-resolution electron microscopy͞single-particle reconstruction models of TFIID have revealed a trilobed architecture containing a large central cavity that has been conse...

The subunit of eubacterial RNA polymerase is required throughout initiation, but how it communicates with core polymerase (␣ 2 ␤␤) is poorly understood. The present work addresses the location and function of the interface of with core. Our studies suggest that this interface is extensive as mutations in six conserved regions of 70 hinder the ability of to bind core. Direct binding of one of these regions to core can be demonstrated using a peptide-based approach. The same regions, and even equivalent residues, in 32 and 70 alter core interaction, suggesting that 70 family members use homologous residues, at least in part, to interact with core. Finally, the regions of that we identify perform specialized functions, suggesting that different portions of the interface perform discrete roles during transcription initiation.