scholarly journals A distinct assembly pathway of the human 39S late pre-mitoribosome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jingdong Cheng ◽  
Otto Berninghausen ◽  
Roland Beckmann
Keyword(s):  
16S Rrna ◽  
Affinity Purification ◽  
Large Subunit ◽  
Assembly Pathway ◽  
Assembly Factors ◽  
Peptidyltransferase Center

AbstractAssembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.

scholarly journals A distinct assembly pathway of the human 39S late pre-mitoribosome

2021 ◽  
Author(s):  
Jingdong Cheng ◽  
Otto Berninghausen ◽  
Roland Beckmann
Keyword(s):  
16S Rrna ◽  
Large Subunit ◽  
Assembly Pathway ◽  
Assembly Factors ◽  
Peptidyltransferase Center

Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. However, little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solved cryo-EM structures of the human 39S large subunit pre-ribosomes, representing four distinct late state intermediates. Besides the MALSU1 complex, we identified several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involved rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we found deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.

scholarly journals Human GTPBP5 (MTG2) fuels mitoribosome large subunit maturation by facilitating 16S rRNA methylation

2020 ◽  
Vol 48 (14) ◽  
pp. 7924-7943 ◽  
Author(s):  
Priyanka Maiti ◽  
Hana Antonicka ◽  
Anne-Claude Gingras ◽  
Eric A Shoubridge ◽  
Antoni Barrientos
Keyword(s):  
Quality Control ◽  
16S Rrna ◽  
Large Subunit ◽  
Mitochondrial Protein ◽  
Small Gtpases ◽  
Mitochondrial Protein Synthesis ◽  
Mitochondrial Ribosomes ◽  
Family Protein ◽  
Assembly Factors ◽  
Subunit Joining

Abstract Biogenesis of mammalian mitochondrial ribosomes (mitoribosomes) involves several conserved small GTPases. Here, we report that the Obg family protein GTPBP5 or MTG2 is a mitochondrial protein whose absence in a TALEN-induced HEK293T knockout (KO) cell line leads to severely decreased levels of the 55S monosome and attenuated mitochondrial protein synthesis. We show that a fraction of GTPBP5 co-sediments with the large mitoribosome subunit (mtLSU), and crosslinks specifically with the 16S rRNA, and several mtLSU proteins and assembly factors. Notably, the latter group includes MTERF4, involved in monosome assembly, and MRM2, the methyltransferase that catalyzes the modification of the 16S mt-rRNA A-loop U1369 residue. The GTPBP5 interaction with MRM2 was also detected using the proximity-dependent biotinylation (BioID) assay. In GTPBP5-KO mitochondria, the mtLSU lacks bL36m, accumulates an excess of the assembly factors MTG1, GTPBP10, MALSU1 and MTERF4, and contains hypomethylated 16S rRNA. We propose that GTPBP5 primarily fuels proper mtLSU maturation by securing efficient methylation of two 16S rRNA residues, and ultimately serves to coordinate subunit joining through the release of late-stage mtLSU assembly factors. In this way, GTPBP5 provides an ultimate quality control checkpoint function during mtLSU assembly that minimizes premature subunit joining to ensure the assembly of the mature 55S monosome.

Phylogeny of the Australian freshwater crayfish Cherax destructor-complex (Decapoda : Parastacidae) inferred from four mitochondrial gene regions

2005 ◽  
Vol 19 (3) ◽  
pp. 209 ◽  
Author(s):  
Thuy T. T. Nguyen ◽  
Christopher M. Austin
Keyword(s):  
16S Rrna ◽  
Cytochrome Oxidase ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
Strong Support ◽  
Interspecific Variation ◽  
Rrna Gene ◽  
Freshwater Crayfish ◽  
Cherax Destructor ◽  
Australian Freshwater

The phylogenetic relationships among 32 individuals of Australian freshwater crayfish belonging to the Cherax destructor-complex were investigated using a dataset comprising sequences from four mitochondrial gene regions: the large subunit rRNA (16S rRNA), cytochrome oxidase I (COI), adenosine triphosphatase 6 (ATPase 6), and cytochrome oxidase III (COIII). A total of 1602 bp was obtained, and a combined analysis of the data produced a tree with strong support (bootstrap values 94–100%) for three divergent lineages, verifying the phylogenetic hypotheses of relationships within the C. destructor species-complex suggested in previous studies. Overall, sequences from the 16S rRNA gene showed the least variation compared to those generated from protein coding genes, which presented considerably greater levels of divergence. The level of divergence within C. destructor was found to be greater than that observed in other species of freshwater crayfish, but interspecific variation among species examined in the present study was similar to that reported previously.

scholarly journals Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium

Microbiology ◽  
2006 ◽  
Vol 152 (7) ◽  
pp. 2159-2169 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Elizaveta M. Spiridonova ◽  
Ivan A. Berg ◽  
Boris B. Kuznetsov ◽  
Dimitry Yu. Sorokin
Keyword(s):  
16S Rrna ◽  
Large Subunit ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Phylogenetic Cluster ◽  
New Family ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Sulfur Oxidizing ◽  
Phylogeny And Evolution

The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin–Benson–Bassham cycle of autotrophic CO2 fixation, was investigated in the members of the genus Thiomicrospira and the relative genus Thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing Gammaproteobacteria. The cbbL gene encoding the ‘green-like’ form I RubisCO large subunit was found in all analysed species, while the cbbM gene encoding form II RubisCO was present only in Thiomicrospira species. Furthermore, species belonging to the Thiomicrospira crunogena 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, cbbL-1 and cbbL-2. Both 16S-rRNA- and cbbL-based phylogenies of the Thiomicrospira–Thioalkalimicrobium–Hydrogenovibrio group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.

scholarly journals MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome

2014 ◽  
Vol 25 (17) ◽  
pp. 2542-2555 ◽  
Author(s):  
Joanna Rorbach ◽  
Pierre Boesch ◽  
Payam A. Gammage ◽  
Thomas J. J. Nicholls ◽  
Sarah F. Pearce ◽  
...  
Keyword(s):  
16S Rrna ◽  
Rna Processing ◽  
Large Subunit ◽  
Peptidyl Transferase ◽  
Mitochondrial Translation ◽  
Peptidyl Transferase Center ◽  
Mitochondrial Ribosome ◽  
Translation Apparatus ◽  
Rrna Maturation ◽  
And Function

Defects of the translation apparatus in human mitochondria are known to cause disease, yet details of how protein synthesis is regulated in this organelle remain to be unveiled. Ribosome production in all organisms studied thus far entails a complex, multistep pathway involving a number of auxiliary factors. This includes several RNA processing and modification steps required for correct rRNA maturation. Little is known about the maturation of human mitochondrial 16S rRNA and its role in biogenesis of the mitoribosome. Here we investigate two methyltransferases, MRM2 (also known as RRMJ2, encoded by FTSJ2) and MRM3 (also known as RMTL1, encoded by RNMTL1), that are responsible for modification of nucleotides of the 16S rRNA A-loop, an essential component of the peptidyl transferase center. Our studies show that inactivation of MRM2 or MRM3 in human cells by RNA interference results in respiratory incompetence as a consequence of diminished mitochondrial translation. Ineffective translation in MRM2- and MRM3-depleted cells results from aberrant assembly of the large subunit of the mitochondrial ribosome (mt-LSU). Our findings show that MRM2 and MRM3 are human mitochondrial methyltransferases involved in the modification of 16S rRNA and are important factors for the biogenesis and function of the large subunit of the mitochondrial ribosome.

scholarly journals Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit

2020 ◽  
Author(s):  
Victor Tobiasson ◽  
Ondřej Gahura ◽  
Shintaro Aibara ◽  
Rozbeh Baradaran ◽  
Alena Zíková ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Acyl Carrier Protein ◽  
Large Subunit ◽  
Structural Characterisation ◽  
Protein Mass ◽  
Assembly Factors ◽  
Mammalian Genomes ◽  
Exit Tunnel ◽  
Protein Components ◽  
Assembly Intermediate

AbstractMitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes with reduced RNA and increased protein mass from Trypanosoma brucei, to provide insights into the biogenesis of mitoribosomal large subunit. Structural characterisation of a stable assembly intermediate revealed 22 assembly factors, some of which are also encoded in mammalian genomes. The assembly factors form a protein network that spans over 180 Å, shielding the ribosomal RNA surface. The entire central protuberance and L7/L12 stalk are not assembled, and require removal of the factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly, while the exit tunnel is blocked. Together, the extensive network of the factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.

Mutually exclusive synthetic pathways for sea urchin mitochondrial rRNA and mRNA

1989 ◽  
Vol 9 (3) ◽  
pp. 1069-1082
Author(s):  
D J Elliott ◽  
H T Jacobs
Keyword(s):  
16S Rrna ◽  
Sea Urchin ◽  
Large Subunit ◽  
Blot Hybridization ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Rna ◽  
Coding Region ◽  
Alternative Processing ◽  
Nadh Dehydrogenase Subunit 2

The structure and abundance of mitochondrial transcripts in sea urchin embryos were investigated by a combination of RNA blot-hybridization, S1 mapping, and primer extension assays. Between the egg and blastula stages, the relative abundance of mitochondrial rRNAs declined slightly, while that of mitochondrial mRNAs increased up to 10-fold. Fine mapping of the termini of the rRNAs and of the adjacent transcripts indicated that, although they appeared to be butt-joined at their 5' ends to the upstream transcripts, tRNA-Phe 5' to the small subunit (12S) rRNA and NADH dehydrogenase subunit 2 mRNA 5' to the large subunit (16S) rRNA, respectively, their 3' ends were found to overlap the 5' ends of the downstream transcripts. 12S rRNA was found to extend 7 to 13 nucleotides into the sequence of tRNA-Glu; 16S rRNA was shown to terminate 3 to 5 nucleotides inside the coding region of cytochrome oxidase subunit 1 (COI) and 8 to 10 nucleotides from the mapped 5' end of COI mRNA. The rRNAs and the downstream transcripts must therefore be synthesized by distinct pathways, either by alternative processing of the same primary transcript(s) or by processing of different precursors. In either case, the events which select the ribosomal 3' ends preclude the production of functional transcripts of the downstream genes from the same precursor molecule. No developmental alterations in transcript structure were detected. We propose that mitochondrial RNA levels are regulated in early development by the selection of alternate and mutually exclusive RNA-processing pathways.

scholarly journals Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2387-2398 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Elizaveta M. Spiridonova ◽  
Ivan A. Berg ◽  
Natalia V. Slobodova ◽  
Eugenia S. Boulygina ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Large Subunit ◽  
Nifh Gene ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Purple Sulfur Bacterium ◽  
The Family

The occurrence of genes encoding nitrogenase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) was investigated in the members of the family Ectothiorhodospiraceae. This family forms a separate phylogenetic lineage within the Gammaproteobacteria according to 16S rRNA gene sequence analysis and mostly includes photo- and chemoautotrophic halophilic and haloalkaliphilic bacteria. The cbbL gene encoding the large subunit of ‘green-like’ form I RubisCO was found in all strains, except the type strains of Alkalispirillum mobile and Arhodomonas aquaeolei. The nifH gene encoding nitrogenase reductase was present in all investigated species of the phototrophic genera Ectothiorhodospira, Halorhodospira and Thiorhodospira, but not of the genus Ectothiorhodosinus. Unexpectedly, nifH fragments were also obtained for the chemotrophic species Thioalkalispira microaerophila and Alkalilimnicola halodurans, for which diazotrophic potential has not previously been assumed. The cbbL-, nifH- and 16S rRNA gene-based trees were not highly congruent in their branching patterns since, in the ‘RubisCO’ and ‘nitrogenase’ trees, representatives of the Ectothiorhodospiraceae are divided in a number of broadly distributed clusters and branches. However, the data obtained may be regarded as evidence of the monophyletic origin of the cbbL and nifH genes in most species within the family Ectothiorhodospiraceae and mainly corresponded to the current taxonomic structure of this family. The cbbL phylogeny of the chemolithoautotrophic sulfur-oxidizers Thioalkalivibrio nitratireducens and Thioalkalivibrio paradoxus and the nitrifier Nitrococcus mobilis deviated significantly from the 16S-rRNA gene-based phylogeny. These species clustered with one of the duplicated cbbL genes of the purple sulfur bacterium Allochromatium vinosum, a member of the family Chromatiaceae.

scholarly journals Diversity of Bacterial Photosymbionts in Lubomirskiidae Sponges from Lake Baikal

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Nina V. Kulakova ◽  
Natalia N. Denikina ◽  
Sergei I. Belikov
Keyword(s):  
16S Rrna ◽  
Lake Baikal ◽  
Large Subunit ◽  
Molecular Approach ◽  
Freshwater Sponge ◽  
Phylogenetic Groups ◽  
Bisphosphate Carboxylase ◽  
Sponge Symbionts

Sponges are permanent benthos residents which establish complex associations with a variety of microorganisms that raise interest in the nature of sponge-symbionts interactions. A molecular approach, based on the identification of the 16S rRNA and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit genes, was applied to investigate diversity and phylogeny of bacterial phototrophs associated with four species of Lubomirskiidae in Lake Baikal. The phylogeny inferred from both genes showed three main clusters of Synechococcus associated with Baikalian sponges. One of the clusters belonged to the cosmopolitan Synechococcus rubescens group and the two other were not related to any of the assigned phylogenetic groups but placed as sister clusters to S. rubescens. These results expanded the understanding of freshwater sponge-associated photoautotroph diversity and suggested that the three phylogenetic groups of Synechococcus are common photosynthetic symbionts in Lubomirskiidae sponges.

Sign in / Sign up

Export Citation Format

Share Document