Researchers Discover the Mitochondrial Equivalent of the Nucleolus

Despite the biological relevance of the mitoribosomes, knowledge about the molecular details of the assembly pathway, co-factors involved in their biogenesis and the submitochondrial compartmentalization of the process is still very limited.

In a study published in the February 12 issue of the journal Cell Reports, a group of University of Miami Miller School of Medicine scientists led by Antoni Barrientos, Ph.D., professor of neurology and biochemistry and molecular biology, discovered a factor that plays an essential role during the early stages of mitoribosome large-subunit assembly. Barrientos and Ya-Ting Tu, a Ph.D. student from the biochemistry and molecular biology program, used human cells in culture to demonstrate that a protein called DDX28 is the first human DEAD-box protein involved in the process of mitoribosome biogenesis.

DDX28 is the homologue of a yeast protein called Mrh4, previously discovered by the Barrientos group and reported in a 2013 study published in Cell Metabolism.

DEAD-box proteins are enzymes that rearrange RNA and RNA-protein structures. Barrientos and his team identified DDX28 as a human mitochondrial DEAD-box protein essential for large mitoribosome subunit biogenesis.

Human mitochondria have one particular ribosome, 55S, consisting of a small 37S subunit and a large 54S subunit. The large subunit is made up of a 15S ribosome RNA (rRNA) and at least 44 proteins. Barrientos and his team demonstrated that the protein DDX28 interacts with the ribosomal 16S RNA of the large subunit to promote its stability and assembly with ribosomal proteins. They silenced the expression of DDX28 in human cultured cells and showed that without DDX28, the 16S rRNA is degraded and the mitoribosome large subunit fails to assemble.

The researchers also created a cell line expressing a tagged version of DDX28 that allowed them to study the DDX28 interactome and its submitochondrial localization. They found that DDX28 accumulate in distinct RNA-containing foci, a group of subcompartments in the mitochondrial matrix originally termed RNA granules. These foci are found in close proximity to the mitochondrial nucleoids, where the mitochondrial DNA (mtDNA) resides. The RNA granules contain all mitoribosomal proteins, factors involved in mitoribosome biogenesis and RNA-metabolism factors.

Barrientos proposes that RNA granules are factories where mitoribosome production occurs. Newly transcribed rRNAs and/or early mitoribosome assembly intermediates are transferred from nucleoids to the RNA granules, where mitoribosome assembly is completed. These mitochondrial matrix sub-compartments are reminiscent of the nucleolus. Within the nucleus, the membrane-less nucleolus is organized around the chromosomal regions that contain the genes for the rRNAs, and is the site of rRNA transcription and processing, and of ribosome assembly. Equivalent features pertain to the mitochondrial RNA granule, which Barrientos’ team proposes to term “mitochondriolus.”

The biomedical importance of the mitochondriolus and the mitoribosomes is highlighted by the fact that mutations affecting mitochondriolus components are responsible for infantile multi-systemic diseases frequently involving encephalomyopathy and hypertrophic cardiomyopathy.

University of Miami