High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes

Krogan, Nevan J.; Peng, Wentao; Cagney, Gerard; Robinson, Mark D.; Haw, Robin; Zhong, Gouqing; Guo, Xinghua; Zhang, Xin; Canadien, Veronica; Richards, Dawn P.; Beattie, Bryan K.; Lalev, Atanas I.; Zhang, Wen; Davierwala, Armaity P.; Mnaimneh, Sanié; Starostine, Andrei; Tikuisis, Aaron; Grigull, Jörg; Datta, Nira; Bray, James E.; Hughes, Timothy R.; Emili, Andrew; Greenblatt, Jack

doi:10.1016/s1097-2765(04)00003-6

Cited by 347 publications

(436 citation statements)

References 65 publications

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“…Early characterization of UTP subcomplexes indicated that Pol5, so named because it bears similarity to DNA polymerases (Shimizu et al 2002), is likely a substoichiometric component of UTP-A (Gallagher et al 2004;Krogan et al 2004). This was not confirmed in recent affinity purifications (Perez-Fernandez et al 2007).…”

Section: Christmas Tree Visualization In Vivo By Ch-ipmentioning

confidence: 99%

“…Preassembled ribosome building blocks likely allow minimizing the huge complexity of ribosome assembly. To date, three SSU-processome subcomplexes have been discriminated structurally and/or functionally: UTP-A (also referred to as t-UTP for transcription UTP), UTP-B (or PWP2), and UTP-C (or CURI), each comprised of z6-7 proteins (Dosil and Bustelo 2004;Gallagher et al 2004;Krogan et al 2004;Perez-Fernandez et al 2007;Rudra et al 2007). UTP-A consists of Utp4, Utp8, Utp9, the HEAT/ Armadillo-repeats Utp10, Utp15, Utp17/Nan1, and Pol5 (Krogan et al 2004).…”

Section: Introductionmentioning

confidence: 99%

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The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance

Wéry¹,

Ruidant²,

Schillewaert³

et al. 2009

RNA

101

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Terminal balls detected at the 59-end of nascent ribosomal transcripts act as pre-rRNA processing complexes and are detected in all eukaryotes examined, resulting in illustrious Christmas tree images. Terminal balls (also known as SSU-processomes) compaction reflects the various stages of cotranscriptional ribosome assembly. Here, we have followed SSU-processome compaction in vivo by use of a chromatin immunoprecipitation (Ch-IP) approach and shown, in agreement with electron microscopy analysis of Christmas trees, that it progressively condenses to come in close proximity to the 59-end of the 25S rRNA gene. The SSU-processome is comprised of independent autonomous building blocks that are loaded onto nascent pre-rRNAs and assemble into catalytically active pre-rRNA processing complexes in a stepwise and highly hierarchical process. Failure to assemble SSU-processome subcomplexes with proper kinetics triggers a nucleolar surveillance pathway that targets misassembled pre-rRNAs otherwise destined to mature into small subunit 18S rRNA for polyadenylation, preferentially by TRAMP5, and degradation by the 39 to 59 exoribonucleolytic activity of the Exosome. Trf5 colocalized with nascent pre-rRNPs, indicating that this nucleolar surveillance initiates cotranscriptionally.

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Section: Christmas Tree Visualization In Vivo By Ch-ipmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance

Wéry¹,

Ruidant²,

Schillewaert³

et al. 2009

RNA

101

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“…Eleven unannotated genes gave rise to G1 arrest after promoter shut-off, suggesting they might be involved in some aspect of ribosome biogenesis or protein biosynthesis. Indeed, high-throughput data suggest several of these genes perform such functions: YPR169W encodes a nucleolar protein of unknown function, which interacts with Tpt1p, a protein involved in tRNA splicing (Hazbun et al, 2003;Huh et al, 2003); Ynl313cp is localized to both cytoplasm and nucleus and interacts with proteins involved in RNA processing, ribosomal biogenesis import, and protein metabolism (Gavin et al, 2002;Huh et al, 2003;Krogan et al, 2004); Ynl310cp encodes a protein that interacts with proteins involved in RNA processing (Gavin et al, 2002;Ho et al, 2002;Hazbun et al, 2003); and Yhr020wp is inferred to have tRNA aminoacylation and ligation activity and also affinity-precipitates with Utp13, which is part of the SSU processome involved in pre-18S rRNA processing (Tatusov et al, 2000;Ho et al, 2002). Finally, Ynr046wp has been recently identified as subunit of tRNA methyltransferase (Purushothaman et al, 2005), and Ynr054cp, which encodes a nucleolar protein that interacts with proteins involved in RNA processing, has been recently characterized as a component of the SSU processome (Gavin et al, 2002;Ho et al, 2002;Huh et al, 2003;Hoang et al, 2005).…”

Section: G1 Phasementioning

confidence: 99%

A Survey of Essential Gene Function in the Yeast Cell Division Cycle

Peña‐Castillo

Mnaimneh

et al. 2006

MBoC

Self Cite

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Mutations impacting specific stages of cell growth and division have provided a foundation for dissecting mechanisms that underlie cell cycle progression. We have undertaken an objective examination of the yeast cell cycle through flow cytometric analysis of DNA content in TetO 7 promoter mutant strains representing 75% of all essential yeast genes. More than 65% of the strains displayed specific alterations in DNA content, suggesting that reduced function of an essential gene in most cases impairs progression through a specific stage of the cell cycle. Because of the large number of essential genes required for protein biosynthesis, G1 accumulation was the most common phenotype observed in our analysis. In contrast, relatively few mutants displayed S-phase delay, and most of these were defective in genes required for DNA replication or nucleotide metabolism. G2 accumulation appeared to arise from a variety of defects. In addition to providing a global view of the diversity of essential cellular processes that influence cell cycle progression, these data also provided predictions regarding the functions of individual genes: we identified four new genes involved in protein trafficking (NUS1, PHS1, PGA2, PGA3), and we found that CSE1 and SMC4 are important for DNA replication. INTRODUCTIONCell division is a fundamental biological process that in all organisms consists of a series of closely coordinated events. In the budding yeast Saccharomyces cerevisiae, the cell division cycle begins with an initial growth phase, G1, during which time the cell increases in mass and volume. The transition from G1 into S phase is marked by progression through Start (the point of commitment to cell division), initiation of nuclear DNA synthesis, and the emergence of a bud that will form the new daughter cell. S phase is followed by a second growth phase, G2, which is in turn followed by nuclear division, and then cell separation. A very similar series of events occurs in all eukaryotes, with the obvious exception of bud emergence. Because of the fundamental biological importance of cell cycle progression and its importance in both human development and diseases such as cancer, identification of the molecular determinants of specific stages of the eukaryotic cell cycle has been a subject of intense study for several decades.The morphological landmarks of the cell cycle stages in budding yeast, most notably the size of the bud relative to the size of the mother cell, allows the identification of mutants blocked at specific stages of the cell cycle and thereby forms the basis for the classic cell cycle screens (Hartwell et al., 1970;Culotti and Hartwell, 1971;Hartwell, 1971aHartwell, , 1971bHartwell, , 1973Moir et al., 1982). These genetic screens, using conditional temperature-sensitive mutants, identified more than 50 genes that are required for specific stages in the cell division cycle and so were termed CDC genes. On average 4.6 alleles were identified for each CDC gene in the original screens, suggesting the number of cdc mutan...

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“…Second, ScDIS3, but no core subunit, was isolated as a high-copy suppressor of the rrp6⌬ slow-growth phenotype (Abruzzi et al, 2007). Third, yeast Rrp6 and Dis3 have interaction partners that are not shared with core subunits (Noguchi et al, 1996;Gavin et al, 2002Gavin et al, , 2006Krogan et al, 2004;Vanacova et al, 2005). Fourth, a yeast mutant Rrp6 polypeptide that no longer interacts with the core exosome retains its 3Ј end processing activities on rRNA and snoRNA transcripts (Callahan and Butler, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Second, ScDIS3, but no core subunit, was isolated as a high-copy suppressor of the rrp6⌬ slow-growth phenotype (Abruzzi et al, 2007). Third, yeast Rrp6 and Dis3 have interaction partners that are not shared with core subunits (Noguchi et al, 1996;Gavin et al, 2002Gavin et al, , 2006Krogan et al, 2004;Vanacova et al, 2005 (Ohkura et al, 1988;Kinoshita et al, 1991;Fomproix and Hernandez-Verdun, 1999). The only core subunit linked to these phenomena is Csl4 (Baker et al, 1998) and that effect has been shown to be indirect (van Hoof et al, 2000).…”

mentioning

confidence: 99%

Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression

Graham

Kiss²,

Andrulis

2009

MBoC

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Exosome complexes are 3 to 5 exoribonucleases composed of subunits that are critical for numerous distinct RNA metabolic (ribonucleometabolic) pathways. Several studies have implicated the exosome subunits Rrp6 and Dis3 in chromosome segregation and cell division but the functional relevance of these findings remains unclear. Here, we report that, in Drosophila melanogaster S2 tissue culture cells, dRrp6 is required for cell proliferation and error-free mitosis, but the core exosome subunit Rrp40 is not. Micorarray analysis of dRrp6-depleted cell reveals increased levels of cell cycleand mitosis-related transcripts. Depletion of dRrp6 elicits a decrease in the frequency of mitotic cells and in the mitotic marker phospho-histone H3 (pH3), with a concomitant increase in defects in chromosome congression, separation, and segregation. Endogenous dRrp6 dynamically redistributes during mitosis, accumulating predominantly but not exclusively on the condensed chromosomes. In contrast, core subunits localize predominantly to MTs throughout cell division. Finally, dRrp6-depleted cells treated with microtubule poisons exhibit normal kinetochore recruitment of the spindle assembly checkpoint protein BubR1 without restoring pH3 levels, suggesting that these cells undergo premature chromosome condensation. Collectively, these data support the idea that dRrp6 has a core exosome-independent role in cell cycle and mitotic progression. INTRODUCTIONExosome complexes are critical players in the processing and degradation of many RNA species (Houseley et al., 2006). Found in both archaebacteria and eukaryotes, these complexes are composed of a "core" set of subunits. With respect to the yeast and human core complexes, they consist of six RNase PH domain-containing proteins (Rrp41, Rrp42, Rrp43, Rrp45, Rrp46, and Mtr3) and three S1 domain-containing proteins (Rrp4, Rrp40, and Csl4). Our understanding of exosome complex form and function has advanced greatly though the report of the crystal structures of archaebacterial (Buttner et al., 2005; and eukaryotic exosome core (Liu et al., 2006) complexes. The RNase PH subunits assemble into a hexameric ring upon which the S1 domain subunits reside. It has been proposed that the cylindrical shape and central channel of exosome complexes have evolved as a means to tightly regulate RNA recognition and subsequent decay (Lorentzen and Conti, 2006).Eukaryotes have compartment-specific exosome subunits and cofactors in addition to the core subunits. Although the eubacterial RNase R homolog Dis3 (also referred to as Rrp44) interacts with the yeast core (Mitchell et al., 1997;Allmang et al., 1999b;Dziembowski et al., 2007), it does not associate with either the human or trypanosome core (Chen et al., 2001;Estevez et al., 2003). Moreover, many archaebacteria lack an RNase R-like protein (Koonin et al., 2001). Thus, strictly speaking, Dis3 is not a core exosome component. Another exosome subunit missing in archaebacteria but present in eukaryotes is Rrp6, an RNase D homolog. Rrp6 associates specifical...

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High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes

Cited by 347 publications

References 65 publications

The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance

The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance

A Survey of Essential Gene Function in the Yeast Cell Division Cycle

Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression

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