Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy

Guo, Qiang; Yuan, Yi; Xu, Yu; Feng, Boya; Liu, Liang; Chen, Kai; Sun, Ming; Yang, Zhixiu; Lei, Jianlin; Gao, Ning

doi:10.1073/pnas.1104645108

Cited by 56 publications

(85 citation statements)

References 51 publications

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“…While this paper was under review another study describing the cryo-EM structure of the YjeQ in complex with the 30S ribosomal subunit was published (Guo et al 2011). …”

Section: Acknowledgmentsmentioning

confidence: 99%

Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor

Jomaa¹,

Stewart²,

Mears³

et al. 2011

RNA

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YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ binds tightly and stoichiometrically to the 30S subunit, which stimulates its GTPase activity by 160-fold. Despite growing evidence for the involvement of the YjeQ protein in bacterial 30S subunit assembly, the specific function and mechanism of this protein remain unclear. Here, we report the costructure of YjeQ with the 30S subunit obtained by cryo-electron microscopy. The costructure revealed that YjeQ interacts simultaneously with helix 44, the head and the platform of the 30S subunit. This binding location of YjeQ in the 30S subunit suggests a chaperone role in processing of the 39 end of the rRNA as well as in mediating the correct orientation of the main domains of the 30S subunit. In addition, the YjeQ binding site partially overlaps with the interaction site of initiation factors 2 and 3, and upon binding, YjeQ covers three inter-subunit bridges that are important for the association of the 30S and 50S subunits. Hence, our structure suggests that YjeQ may assist in ribosome maturation by preventing premature formation of the translation initiation complex and association with the 50S subunit. Together, these results support a role for YjeQ in the late stages of 30S maturation.

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“…While this paper was under review another study describing the cryo-EM structure of the YjeQ in complex with the 30S ribosomal subunit was published (Guo et al 2011). …”

Section: Acknowledgmentsmentioning

confidence: 99%

Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor

Jomaa¹,

Stewart²,

Mears³

et al. 2011

RNA

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“…Their roles in the maturation of the functional core of the 30S subunit may entail facilitating proper 17S rRNA folding, assisting processing of the rRNA, or mediating protein-RNA interactions. Cryo-electron microscopy (cryo-EM) (Sharma et al 2005;Datta et al 2007;Guo et al 2011;Jomaa et al 2011b) revealed that at least three factors, Era, YjeQ, and RbfA bind at or in close proximity to the decoding center at sites that are not overlapping, indicating that simultaneous binding is stereochemically possible. Consistently, genetic experiments (Bylund et al 1998(Bylund et al , 2001Inoue et al 2003Inoue et al , 2006Campbell and Brown 2008) suggested that these factors operate in conjunction rather than independently.…”

Section: Introductionmentioning

confidence: 99%

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

Jeganathan

Razi

Thurlow

2015

RNA

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YjeQ (also called RsgA) and RbfA proteins in Escherichia coli bind to immature 30S ribosome subunits at late stages of assembly to assist folding of the decoding center. A key step for the subunit to enter the pool of actively translating ribosomes is the release of these factors. YjeQ promotes dissociation of RbfA during the final stages of maturation; however, the mechanism implementing this functional interplay has not been elucidated. YjeQ features an amino-terminal oligonucleotide/oligosaccharide binding domain, a central GTPase module and a carboxy-terminal zinc-finger domain. We found that the zinc-finger domain is comprised of two functional motifs: the region coordinating the zinc ion and a carboxy-terminal α-helix. The first motif is essential for the anchoring of YjeQ to the 30S subunit and the carboxy-terminal α-helix facilitates the removal of RbfA once the 30S subunit reaches the mature state. Furthermore, the ability of the mature 30S subunit to stimulate YjeQ GTPase activity also depends on the carboxy-terminal α-helix. Our data are consistent with a model in which YjeQ uses this carboxy-terminal α-helix as a sensor to gauge the conformation of helix 44, an essential motif of the decoding center. According to this model, the mature conformation of helix 44 is sensed by the carboxy-terminal α-helix, which in turn stimulates the YjeQ GTPase activity. Hydrolysis of GTP is believed to assist the release of YjeQ from the mature 30S subunit through a still uncharacterized mechanism. These results identify the structural determinants in YjeQ that implement the functional interplay with RbfA.

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“…Structurally, it has been shown that YjeQ, RbfA, and Era all bind in close proximity to the decoding center of the mature 30S subunit (Sharma et al 2005;Datta et al 2007;Guo et al 2011;Jomaa et al 2011b), suggesting that these factors play a joint role in the organization of the functional core of the small subunit. Genetic evidence suggests that RimM binds to a distinct region of the head of the 30S subunit comprised of helices 31 and 33b of the 16S rRNA and r-proteins S13 and S19 right above the decoding center (Lovgren et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement

Leong

Kent

Jomaa

et al. 2013

RNA

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Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of the maturation process of the small subunit. However, it is unclear how the functional interplay between these factors occurs in the context of multiple parallel pathways. To understand how these factors work together, we have characterized the immature 30S subunits that accumulate in ΔrimM cells and compared them with immature 30S subunits from a ΔyjeQ strain. The cryo-EM maps obtained from these particles showed that the densities representing helices 44 and 45 in the rRNA were partially missing, suggesting mobility of these motifs. These 30S subunits were also partially depleted in all tertiary ribosomal proteins, particularly those binding in the head domain. Using image classification, we identified four subpopulations of ΔrimM immature 30S subunits differing in the amount of missing density for helices 44 and 45, as well as the amount of density existing in these maps for the underrepresented proteins. The structural defects found in these immature subunits resembled those of the 30S subunits that accumulate in the ΔyjeQ strain. These findings are consistent with an "early convergency model" in which multiple parallel assembly pathways of the 30S subunit converge into a late assembly intermediate, as opposed to the mature state. Functionally related factors will bind to this intermediate to catalyze the last steps of maturation leading to the mature 30S subunit.

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Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy

Cited by 56 publications

References 51 publications

Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor

Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor

The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly

Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement

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