Mutations in the mitochondrial DNA are relatively common, affecting one in a few thousand people, and are linked to common illnesses along with a wide range of fatal or progressively debilitating diseases, including diabetes, gastrointestinal disorders, heart disease, dementia, deafness, and eye disorders.
But now there are new reasons to suspect their roles in disorders.
In their new study, published in the journal Mitochondrion, the researchers have shown for the first time that human mitochondrial DNA leaves the mitochondria, travels into the host cell nucleus and connects to specific genes.
"We found evidence that mitochondria DNA and nuclear DNA 'talk to each other', and these interactions aren't random," said lead researcher Dr Justin O'Sullivan, a Liggins molecular geneticist.
The findings give weight to the idea that mitochondria do much more than supply energy and regulate a cell's metabolism - the processes that keep it alive.
"We think the connections we detected are part of a feedback system between mitochondria and the cell nucleus that may influence how humans grow and develop throughout life," O'Sullivan said.
"We know that these connections between mitochondrial and nuclear DNA can influence how the nuclear genes work in yeast, and we speculate that the same occurs in humans."
Interactions between the two sets of DNA within our cells could be one of the ways the environment influences gene expression, he said.
One theory about mitochondrial disease is that damaged mitochondria fail to supply enough energy to the cell so it can't work properly.
But this latest finding suggests another possible culprit: problems with the way the mitochondrial and nuclei DNA "talk" to each other - or fail to talk to each other.
"Mitochondrial dysfunction is linked to highly prevalent diseases such as obesity, diabetes, cancer and heart disease," said study co-author Associate Professor Mark Vickers, also from the Liggins Institute.
"This study adds to our understanding of the way in which changes to mitochondria manifest as disease."
Further research could yield new treatment avenues, he said.
The scientists now need to figure out exactly how the two sets of DNA talk to each other - and what happens when they do.
The new study follows another landmark discovery by scientists at Wellington's Malaghan Institute, who last year became the first in the world to demonstrate the movement of mitochondrial DNA between cells in an animal tumour.
DNA insights
• Mitochondria are tiny, specialised sub-units of cells that act as cell "generators" and regulate cell metabolism. They pass down the maternal line and have their own small set of DNA.
• Researchers have shown for the first time in humans that mitochondrial DNA travels into the host cell nucleus and "talks to" specific genes on the DNA.
• Mitochondrial DNA may influence gene expression. This finding could be a key to understanding how mitochondrial DNA mutations manifest as disease.