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Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes.

Jakob S, Ohmayer U, Neueder A, Hierlmeier T, Perez-Fernandez J, Hochmuth E, Deutzmann R, Griesenbeck J, Tschochner H, Milkereit P - PLoS ONE (2012)

Bottom Line: One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain.Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes.They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany.

ABSTRACT
Early steps of eukaryotic ribosome biogenesis require a large set of ribosome biogenesis factors which transiently interact with nascent rRNA precursors (pre-rRNA). Most likely, concomitant with that initial contacts between ribosomal proteins (r-proteins) and ribosome precursors (pre-ribosomes) are established which are converted into robust interactions between pre-rRNA and r-proteins during the course of ribosome maturation. Here we analysed the interrelationship between r-protein assembly events and the transient interactions of ribosome biogenesis factors with early pre-ribosomal intermediates termed 90S pre-ribosomes or small ribosomal subunit (SSU) processome in yeast cells. We observed that components of the SSU processome UTP-A and UTP-B sub-modules were recruited to early pre-ribosomes independently of all tested r-proteins. On the other hand, groups of SSU processome components were identified whose association with early pre-ribosomes was affected by specific r-protein assembly events in the head-platform interface of the SSU. One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain. Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes. They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.

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30S in vitro assembly map ordered in accordance to the domain organisation of the 16S rRNA and represented in a 2D projection of the 30S ribosomal subunit (adapted from [4]).(A) The six different r-protein assembly trees (initiated by primary binding r-proteins) of the E. coli 30S subunit are ordered according to their physical location on the 16S rRNA (in 5′ to 3′ direction) and attributed to 16S rRNA domain organisation (5′, central, and 3′ domain). The r-proteins are classified by their binding hierarchy. Primary binding proteins (1°) are capable of initiating pioneering interactions with rRNA independent of other proteins. The secondary binders (2°) require one or more primary binding proteins for their association with rRNA, while tertiary binding (3°) proteins require both primary and secondary binders for their incorporation into ribosomal subunits. If existing, homologous r-proteins in S. cerevisiae (rpS nomenclature) are shown next to their prokaryotic counterparts. (B) A schematic presentation of the tertiary structure of the 16S rRNA is depicted. Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the 30S subunit. The 16S rRNA 5′ domain forms the shoulder and foot (red), the central domain forms the platform (green) and the 3′ major domain forms the head (blue). The assembly map of (A) is superimposed in this schematic structure visualisation paying attention to the localisation of the respective r-protein. The colour of the circle gives information about the assembly hierarchy of the respective r-protein (see also A). S11/rpS14 is classified in a species-dependent manner as a tertiary binder (E. coli) or a primary binder (Aquifex aeolicus) [60]. Only r-proteins with sequence homologous in S. cerevisiae (rpS nomenclature) are shown. The figure is reproduced and adapted from [4] (adaptation from the original assembly map of Nomura and colleagues [1]).
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pone-0032552-g001: 30S in vitro assembly map ordered in accordance to the domain organisation of the 16S rRNA and represented in a 2D projection of the 30S ribosomal subunit (adapted from [4]).(A) The six different r-protein assembly trees (initiated by primary binding r-proteins) of the E. coli 30S subunit are ordered according to their physical location on the 16S rRNA (in 5′ to 3′ direction) and attributed to 16S rRNA domain organisation (5′, central, and 3′ domain). The r-proteins are classified by their binding hierarchy. Primary binding proteins (1°) are capable of initiating pioneering interactions with rRNA independent of other proteins. The secondary binders (2°) require one or more primary binding proteins for their association with rRNA, while tertiary binding (3°) proteins require both primary and secondary binders for their incorporation into ribosomal subunits. If existing, homologous r-proteins in S. cerevisiae (rpS nomenclature) are shown next to their prokaryotic counterparts. (B) A schematic presentation of the tertiary structure of the 16S rRNA is depicted. Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the 30S subunit. The 16S rRNA 5′ domain forms the shoulder and foot (red), the central domain forms the platform (green) and the 3′ major domain forms the head (blue). The assembly map of (A) is superimposed in this schematic structure visualisation paying attention to the localisation of the respective r-protein. The colour of the circle gives information about the assembly hierarchy of the respective r-protein (see also A). S11/rpS14 is classified in a species-dependent manner as a tertiary binder (E. coli) or a primary binder (Aquifex aeolicus) [60]. Only r-proteins with sequence homologous in S. cerevisiae (rpS nomenclature) are shown. The figure is reproduced and adapted from [4] (adaptation from the original assembly map of Nomura and colleagues [1]).

Mentions: Prokaryotic ribosomes consist of three ribosomal RNAs (rRNAs) and ∼55 ribosomal proteins (r-proteins). In vitro assembly of prokaryotic ribosomes may occur in the absence of auxiliary factors and follows hierarchical principles [1]–[4]. Primary binding r-proteins are capable of initiating interactions with the rRNA independently of other proteins. Secondary binders require one or more primary binding proteins for their stable association with rRNA, while tertiary binding proteins require both primary and secondary binders for their efficient incorporation into ribosomal subunits. According to the primary binding event, r-proteins of the small ribosomal subunit (SSU) can be grouped into six different assembly trees, each of which assembles in a cooperative manner. R-proteins of three of these assembly trees bind to the 5′ secondary structure domain of the prokaryotic 16S SSU rRNA, r-proteins of two other assembly trees bind to the central domain, and r-proteins of the sixth assembly tree bind to the 3′ major domain (see Fig. 1). Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the SSU: the 5′ domain forms the shoulder and the foot, the central domain forms the platform and the 3′ major domain forms the head. Remarkably, these three major SSU rRNA domains can largely assemble in vitro with corresponding r-proteins independently of each other [5]–[7]. More recently, time resolved hydroxyl radical footprinting analyses showed that some of the contacts of r-proteins with the 16S rRNA can already be observed very soon after initiating prokaryotic SSU in vitro assembly reactions [8]. The establishment of other contacts, however, was substantially slower, probably driven by induced fit mechanisms.


Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes.

Jakob S, Ohmayer U, Neueder A, Hierlmeier T, Perez-Fernandez J, Hochmuth E, Deutzmann R, Griesenbeck J, Tschochner H, Milkereit P - PLoS ONE (2012)

30S in vitro assembly map ordered in accordance to the domain organisation of the 16S rRNA and represented in a 2D projection of the 30S ribosomal subunit (adapted from [4]).(A) The six different r-protein assembly trees (initiated by primary binding r-proteins) of the E. coli 30S subunit are ordered according to their physical location on the 16S rRNA (in 5′ to 3′ direction) and attributed to 16S rRNA domain organisation (5′, central, and 3′ domain). The r-proteins are classified by their binding hierarchy. Primary binding proteins (1°) are capable of initiating pioneering interactions with rRNA independent of other proteins. The secondary binders (2°) require one or more primary binding proteins for their association with rRNA, while tertiary binding (3°) proteins require both primary and secondary binders for their incorporation into ribosomal subunits. If existing, homologous r-proteins in S. cerevisiae (rpS nomenclature) are shown next to their prokaryotic counterparts. (B) A schematic presentation of the tertiary structure of the 16S rRNA is depicted. Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the 30S subunit. The 16S rRNA 5′ domain forms the shoulder and foot (red), the central domain forms the platform (green) and the 3′ major domain forms the head (blue). The assembly map of (A) is superimposed in this schematic structure visualisation paying attention to the localisation of the respective r-protein. The colour of the circle gives information about the assembly hierarchy of the respective r-protein (see also A). S11/rpS14 is classified in a species-dependent manner as a tertiary binder (E. coli) or a primary binder (Aquifex aeolicus) [60]. Only r-proteins with sequence homologous in S. cerevisiae (rpS nomenclature) are shown. The figure is reproduced and adapted from [4] (adaptation from the original assembly map of Nomura and colleagues [1]).
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Related In: Results  -  Collection

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pone-0032552-g001: 30S in vitro assembly map ordered in accordance to the domain organisation of the 16S rRNA and represented in a 2D projection of the 30S ribosomal subunit (adapted from [4]).(A) The six different r-protein assembly trees (initiated by primary binding r-proteins) of the E. coli 30S subunit are ordered according to their physical location on the 16S rRNA (in 5′ to 3′ direction) and attributed to 16S rRNA domain organisation (5′, central, and 3′ domain). The r-proteins are classified by their binding hierarchy. Primary binding proteins (1°) are capable of initiating pioneering interactions with rRNA independent of other proteins. The secondary binders (2°) require one or more primary binding proteins for their association with rRNA, while tertiary binding (3°) proteins require both primary and secondary binders for their incorporation into ribosomal subunits. If existing, homologous r-proteins in S. cerevisiae (rpS nomenclature) are shown next to their prokaryotic counterparts. (B) A schematic presentation of the tertiary structure of the 16S rRNA is depicted. Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the 30S subunit. The 16S rRNA 5′ domain forms the shoulder and foot (red), the central domain forms the platform (green) and the 3′ major domain forms the head (blue). The assembly map of (A) is superimposed in this schematic structure visualisation paying attention to the localisation of the respective r-protein. The colour of the circle gives information about the assembly hierarchy of the respective r-protein (see also A). S11/rpS14 is classified in a species-dependent manner as a tertiary binder (E. coli) or a primary binder (Aquifex aeolicus) [60]. Only r-proteins with sequence homologous in S. cerevisiae (rpS nomenclature) are shown. The figure is reproduced and adapted from [4] (adaptation from the original assembly map of Nomura and colleagues [1]).
Mentions: Prokaryotic ribosomes consist of three ribosomal RNAs (rRNAs) and ∼55 ribosomal proteins (r-proteins). In vitro assembly of prokaryotic ribosomes may occur in the absence of auxiliary factors and follows hierarchical principles [1]–[4]. Primary binding r-proteins are capable of initiating interactions with the rRNA independently of other proteins. Secondary binders require one or more primary binding proteins for their stable association with rRNA, while tertiary binding proteins require both primary and secondary binders for their efficient incorporation into ribosomal subunits. According to the primary binding event, r-proteins of the small ribosomal subunit (SSU) can be grouped into six different assembly trees, each of which assembles in a cooperative manner. R-proteins of three of these assembly trees bind to the 5′ secondary structure domain of the prokaryotic 16S SSU rRNA, r-proteins of two other assembly trees bind to the central domain, and r-proteins of the sixth assembly tree bind to the 3′ major domain (see Fig. 1). Each of the three major secondary structure domains of the 16S rRNA forms distinct morphological features of the SSU: the 5′ domain forms the shoulder and the foot, the central domain forms the platform and the 3′ major domain forms the head. Remarkably, these three major SSU rRNA domains can largely assemble in vitro with corresponding r-proteins independently of each other [5]–[7]. More recently, time resolved hydroxyl radical footprinting analyses showed that some of the contacts of r-proteins with the 16S rRNA can already be observed very soon after initiating prokaryotic SSU in vitro assembly reactions [8]. The establishment of other contacts, however, was substantially slower, probably driven by induced fit mechanisms.

Bottom Line: One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain.Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes.They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany.

ABSTRACT
Early steps of eukaryotic ribosome biogenesis require a large set of ribosome biogenesis factors which transiently interact with nascent rRNA precursors (pre-rRNA). Most likely, concomitant with that initial contacts between ribosomal proteins (r-proteins) and ribosome precursors (pre-ribosomes) are established which are converted into robust interactions between pre-rRNA and r-proteins during the course of ribosome maturation. Here we analysed the interrelationship between r-protein assembly events and the transient interactions of ribosome biogenesis factors with early pre-ribosomal intermediates termed 90S pre-ribosomes or small ribosomal subunit (SSU) processome in yeast cells. We observed that components of the SSU processome UTP-A and UTP-B sub-modules were recruited to early pre-ribosomes independently of all tested r-proteins. On the other hand, groups of SSU processome components were identified whose association with early pre-ribosomes was affected by specific r-protein assembly events in the head-platform interface of the SSU. One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain. Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes. They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.

Show MeSH