Rapid evolution in sequence and length of the nuclear-located gene for mitochondrial L2 ribosomal protein in cereals

The L2 ribosomal protein is typically one of the most conserved proteins in the ribosome and is universally present in bacterial, archaeal, and eukaryotic cytosolic and organellar ribosomes. It is usually 260–270 amino acids long and its binding to the large-subunit ribosomal RNA near the peptidyl transferase center is mediated by a β-barrel RNA-binding domain with 10 β strands. In the diverse land plants Marchantia polymorpha (liverwort) and Oryza sativa (rice), the mitochondrial-encoded L2 ribosomal protein is about 500 amino acids long owing to a centrally located expansion containing the β3–β4 strand region. We have determined that, in wheat, the functional rpl2 gene has been trans ferred to the nucleus and much of the plant-specific internal insert has been deleted. Its mRNA is only 1.2 kb, and two expressed copies in wheat encode proteins of 318 and 319 amino acids, so they are considerably shorter than the maize nuclear-located rpl2 gene of 448 codons. Comparative sequence analysis of cereal mitochondrial L2 ribosomal proteins indicates that the mid region has undergone unexpectedly rapid evolution during the last 60 million years.Key words: mitochondria, ribosomal protein, plants, evolutionary gene transfer.

Download Full-text

Simplification of Ribosomes in Bacteria with Tiny Genomes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa184 ◽

2020 ◽

Vol 38 (1) ◽

pp. 58-66 ◽

Cited By ~ 3

Author(s):

Daria D Nikolaeva ◽

Mikhail S Gelfand ◽

Sofya K Garushyants

Keyword(s):

Ribosomal Protein ◽

Ribosomal Rna ◽

Ribosomal Proteins ◽

Protein Biosynthesis ◽

Large Subunit ◽

Protein Composition ◽

Small Subunit ◽

Bacterial Genomes ◽

Shine Dalgarno Sequence

Abstract The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine–Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.

Download Full-text

NAC covers ribosome-associated nascent chains thereby forming a protective environment for regions of nascent chains just emerging from the peptidyl transferase center.

The Journal of Cell Biology ◽

10.1083/jcb.130.3.519 ◽

1995 ◽

Vol 130 (3) ◽

pp. 519-528 ◽

Cited By ~ 91

Author(s):

S Wang ◽

H Sakai ◽

M Wiedmann

Keyword(s):

Amino Acids ◽

Ribosomal Protein ◽

Ribosomal Proteins ◽

Peptidyl Transferase ◽

Nascent Polypeptide ◽

Peptidyl Transferase Center ◽

Protease Resistance ◽

Protective Environment ◽

Cytosolic Factors

We demonstrate that nascent polypeptide-associated complex (NAC) is one of the first cytosolic factors that newly synthesized nascent chains encounter. When NAC is present, nascent chains are segregated from the cytosol until approximately 30 amino acids in length, a finding consistent with the well-documented protease resistance of short ribosome-associated nascent chains. When NAC is removed, the normally protected nascent chains are susceptible to proteolysis. Therefore NAC, by covering COOH-terminal segments of nascent chains on the ribosome, perhaps together with ribosomal proteins, forms a protective environment for regions of nascent chains just emerging from the peptidyl transferase center. Since NAC is not a core ribosomal protein, the emergence of nascent chains from the ribosome may be more dynamic than previously thought.

Download Full-text

Clusters of Basic Amino Acids Contribute to RNA Binding and Nucleolar Localization of Ribosomal Protein L22

PLoS ONE ◽

10.1371/journal.pone.0005306 ◽

2009 ◽

Vol 4 (4) ◽

pp. e5306 ◽

Cited By ~ 16

Author(s):

Jennifer L. Houmani ◽

Ingrid K. Ruf

Keyword(s):

Amino Acids ◽

Ribosomal Protein ◽

Rna Binding ◽

Nucleolar Localization ◽

Basic Amino Acids ◽

Ribosomal Protein L22

Download Full-text

Protein binding and subunit association activity in particles reconstituted from Escherichia coli MRE600 50S ribosomal components

Canadian Journal of Biochemistry ◽

10.1139/o76-067 ◽

1976 ◽

Vol 54 (5) ◽

pp. 470-476

Author(s):

F. K. Chu ◽

P. Y. Maeba

Keyword(s):

Escherichia Coli ◽

Protein Binding ◽

Ribosomal Rna ◽

Ribosomal Proteins ◽

Rna Binding ◽

5S Rna ◽

Ribonucleoprotein Particles ◽

Incubation Method ◽

Do So

Reconstituted 37S and 48S ribonucleoprotein particles were constructed by incubating Escherichia coli ribosomal RNA with total 50S ribosomal proteins by a sequential incubation method. By comparing the protein compositions of the two types of particles, the proteins that bind to 37S complexes to form 48S particles have been determined. Although only 48S particles could associate with 30S subunits, isolated 37S reconstituted particles could do so if incubated with exogenous 50S proteins. The proteins that bind under these conditions and confer upon particles the ability to associate are L2, L11, L15, L18 and L25. The involvement of these proteins in 5S RNA binding is discussed.

Download Full-text

Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution

Biochemistry and Cell Biology ◽

10.1139/o95-105 ◽

1995 ◽

Vol 73 (11-12) ◽

pp. 979-986 ◽

Cited By ~ 18

Author(s):

V. Ramakrishnan ◽

Sue Ellen Gerchman ◽

Jadwiga H. Kycia ◽

Christopher Davies ◽

Barbara L. Golden ◽

...

Keyword(s):

Antibiotic Resistance ◽

High Resolution ◽

Ribosomal Rna ◽

Ribosomal Proteins ◽

Bacillus Stearothermophilus ◽

Rna Binding ◽

X Ray ◽

X Ray Crystallography ◽

Binding Regions

After along hiatus, the pace of determination of the structures of ribosomal proteins has accelerated dramatically. We discuss here the structures of five ribosomal proteins from Bacillus stearothermophilus: S5, S17, L6, L9, and L14. These structures represent several new motifs. Each of these structures has revealed new insights, and we have developed criteria for recognizing RNA-binding regions of each protein and correlating the structures with such properties as antibiotic resistance. The information here should also prove invaluable in an eventual high-resolution picture of the intact ribosome.Key words: ribosome, ribosomal proteins, ribosomal RNA, X-ray crystallography, NMR.

Download Full-text

Modular assembly of the nucleolar large subunit processome

10.1101/223412 ◽

2017 ◽

Cited By ~ 1

Author(s):

Zahra Assur Sanghai ◽

Linamarie Miller ◽

Kelly R. Molloy ◽

Jonas Barandun ◽

Mirjam Hunziker ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Molecular Mimicry ◽

Large Subunit ◽

Ribosome Assembly ◽

Modular Assembly ◽

Assembly Result ◽

Concerted Activity ◽

Folding Pathways ◽

Exit Tunnel

Early co-transcriptional events of eukaryotic ribosome assembly result in the formation of the small and large subunit processomes. We have determined cryo-EM reconstructions of the nucleolar large subunit processome in different conformational states at resolutions up to 3.4 Ångstroms. These structures reveal how steric hindrance and molecular mimicry are used to prevent premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Mutually exclusive conformations of these particles suggest that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly.

Download Full-text

Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast

Nature Communications ◽

10.1038/s41467-021-26207-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Mariam Jaafar ◽

Julia Contreras ◽

Carine Dominique ◽

Sara Martín-Villanueva ◽

Régine Capeyrou ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Ribosomal Subunit ◽

Rna Helicase ◽

Genetic Interactions ◽

Large Ribosomal Subunit ◽

Base Pairing ◽

Peptidyl Transferase ◽

Peptidyl Transferase Center

AbstractSynthesis of eukaryotic ribosomes involves the assembly and maturation of precursor particles (pre-ribosomal particles) containing ribosomal RNA (rRNA) precursors, ribosomal proteins (RPs) and a plethora of assembly factors (AFs). Formation of the earliest precursors of the 60S ribosomal subunit (pre-60S r-particle) is among the least understood stages of ribosome biogenesis. It involves the Npa1 complex, a protein module suggested to play a key role in the early structuring of the pre-rRNA. Npa1 displays genetic interactions with the DExD-box protein Dbp7 and interacts physically with the snR190 box C/D snoRNA. We show here that snR190 functions as a snoRNA chaperone, which likely cooperates with the Npa1 complex to initiate compaction of the pre-rRNA in early pre-60S r-particles. We further show that Dbp7 regulates the dynamic base-pairing between snR190 and the pre-rRNA within the earliest pre-60S r-particles, thereby participating in structuring the peptidyl transferase center (PTC) of the large ribosomal subunit.

Download Full-text

The pseudouridine residues of ribosomal RNA

Biochemistry and Cell Biology ◽

10.1139/o95-099 ◽

1995 ◽

Vol 73 (11-12) ◽

pp. 915-924 ◽

Cited By ~ 46

Author(s):

James Ofengand ◽

Andrei Bakin ◽

Jan Wrzesinski ◽

Kelvin Nurse ◽

Byron G. Lane

Keyword(s):

Ribosomal Rna ◽

Large Subunit ◽

Small Subunit ◽

Modified Nucleosides ◽

Peptidyl Transferase ◽

Functional Roles ◽

Structural Types ◽

Representative Species ◽

Sequencing Technique ◽

Nucleotide Resolution

Pseudouridine (Ψ), the most common single modified nucleoside in ribosomal RNA, has been positioned in the small subunit (SSU) and large subunit (LSU) RNAs of a number of representative species. Most of the information has been obtained by application of a rapid primed reverse transcriptase sequencing technique. The locations of these Ψ residues have been compared. Many sites for Ψ are the same among species, but others are distinct. In general, the percentage Ψ in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the Ψ residues are strongly clustered in three domains, all of which are near or connected to the peptidyl transferase center. There is no apparent clustering of Ψ in SSU RNA. The Ψ sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 Ψ sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 Ψ sites can be classified into five structural types. Two Escherichia coli Ψ synthases have been cloned and characterized, one for Ψ516 in SSU RNA and one for Ψ746 in LSU RNA. The Ψ746 synthase recognizes free RNA, but the Ψ516 enzyme requires an intermediate RNP particle. Possible functional roles for Ψ in the ribosome are discussed.Key words: pseudouridine, sequencing, modified nucleosides, ribosomal RNA.

Download Full-text