Matrix proteases in mitochondrial DNA function

Abstract

Lon, ClpXP and m-AAA are the three major ATP-dependent proteases in the mitochondrial matrix. All three are involved in general quality control by degrading damaged or abnormal proteins. In addition to this role, they are proposed to serve roles in mitochondrial DNA functions including packaging and stability, replication, transcription and translation. In particular, Lon has been implicated in mtDNA metabolism in yeast, fly and humans. Here, we review the role of Lon protease in mitochondrial DNA functions, and discuss a putative physiological role for mitochondrial transcription factor A (TFAM) degradation by Lon protease. We also discuss the possible roles of m-AAA and ClpXP in mitochondrial DNA functions, and the putative candidate substrates for the three matrix proteases. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Figure 1. AAA+ proteases in the mitochondrial matrix

Lon, ClpXP and m-AAA are the three major proteases in the animal mitochondrial matrix. Lon and ClpXP localize in the mitochondrial matrix per se, whereas the m-AAA protease is membrane anchored to expose its catalytic site to the matrix space. Lon forms a ring-shaped homo-oligomeric structure, and m-AAA forms homo- or hetero-oligomeric structures. ClpXP is composed of two subunits, ClpP and ClpX; it is a hetero-oligomeric complex in which ClpP forms a two-stack heptameric ring-shaped structure to which two hexameric ClpX rings bind on each side. Some mitochondrial proteins, such as TFAM, mtDNA replication factors, etc., bind to mtDNA to package it into a structure called the mitochondrial nucleoid. Lon is also a component of the mitochondrial nucleoid.

Figure 2. Domain strucure of the Lon protease

Lon comprises three domains, an N-terminal domain, central AAA+ ATPase domain, and a C-terminal protease domain. The N-terminal domain is involved in oligomerization and protein substrate binding. The AAA+ domain that contributes ATP binding and hydrolysis consists of two sub-domains, an α/β domain and an α domain. The DNA-binding domains in E. coli and B. thermoruber Lon reside in different regions within the AAA+ module, and that in mitochondrial Lon has not been localized. The C-terminal protease domain contains a serine and lysine dyad in the active site.

Figure 3. mtDNA and TFAM function in an interdependent manner

Upper panel, Upon mtDNA depletion, TFAM is degraded by the Lon protease; middle panel, mtDNA and TFAM stabilize each other; lower panel, reduction of TFAM results in depletion of mtDNA.

Figure 4. Lon protease degrades TFAM to stabilize the TFAM: mtDNA ratio

A, Upon reduction of mtDNA copy number in normal cells, Lon degrades TFAM to normalize the TFAM: mtDNA ratio. As a result of this process, mtDNA transcription occurs normally. B, Upon mtDNA reduction in Lon-depleted cells, TFAM is not degraded, resulting in a dramatic increase in the TFAM: mtDNA ratio. This results in a severe inhibition in mtDNA transcription, which is likely caused by mtDNA overpackaging by TFAM. C, Excess TFAM overexpression leads to an increase in the TFAM: mtDNA ratio, resulting in a severe inhibition in mtDNA transcription.

Figure 5. Potential physiological roles of the AAA+ proteases in mtDNA function

The model shows that the three AAA+ proteases in the mitochondrial matrix regulate mitochondrial protein levels to sustain proper mtDNA functions, such as mtDNA packaging and stability, replication, transcription and translation.