Hidaka T, Pandian GN, Taniguchi J, Nobeyama T, Hashiya K,
Bando T, Sugiyama H. Creation of a Synthetic Ligand for Mitochondrial DNA
Sequence Recognition and Promoter-Specific Transcription Suppression. J Am Chem Soc.
2017 Jun 28;139(25):8444-8447.
Abstract
Synthetic ligands capable of recognizing the specific DNA
sequences inside human mitochondria and modulating gene transcription are in
increasing demand because of the surge in evidence linking mitochondrial genome
and diseases. In the work described herein, we created a new type of
mitochondria-specific synthetic ligand, termed MITO-PIPs, by conjugating a
mitochondria-penetrating peptide with pyrrole-imidazole polyamides (PIPs). The
designed MITO-PIPs showed specific localization inside mitochondria in HeLa
cells and recognized the target DNA in a sequence-specific manner. Furthermore,
MITO-PIPs that inhibit the binding of mitochondrial transcription factor A to
the light-strand promoter (LSP) also triggered targeted transcriptional
suppression. The tunability of PIPs' properties suggests the potential of the
MITO-PIPs as potent modulators of not only mitochondrial gene transcription but
also its DNA mutations.
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From the article
Although most mutations in mtDNA have a minimal effect on
cellular function, recent evidence has revealed that some mutations can cause
mitochondrial diseases. Furthermore, the mtDNA haplotype is related to the risk
of other diseases such as diabetes. Whereas patients with Leber’s hereditary
optic neuropathy have a T-to-C mutation in the ND6 gene, patients with Leigh
syndrome have a G-to-A mutation. The mutated mtDNA is a prime target for
disease therapy because a higher percentage of mutated mtDNA exceeding a
threshold can cause cellular defects and mitochondrial diseases. MITO-PIPs
could also read the sequence of a mutated region and distinguish mutated mtDNA
from normal mtDNA. Therefore, MITO-PIPs can be developed further to generate a
new functional compound that can exert bioactivity on either a normal or a
mutated mtDNA in a defined manner. Our proof-of-concept study provides a fresh
platform that opens new avenues for DNA-based functional ligands that are
capable of altering the mitochondrial genome in a sequence-specific manner.
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A new molecule that reads mitochondrial DNA could pave the
way to treat some genetic nerve and muscle diseases
For the first time, a synthetic compound has been made that
can bind to DNA in the cells’ energy powerhouses, suppressing a gene associated
with nerve and muscle disease.
Pyrrole-imidazole polyamides (PIPs) are compounds that can
read specific DNA sequences inside living cells and silence disease-causing
genes. They prevent proteins, called transcription factors, from binding to
specific parts of the DNA strand, thus suppressing the transcription of DNA
into RNA.
Most DNA is found in the nucleus. But mitochondria, the
cell’s powerhouses, also host a small amount of DNA. PIPs are capable of
crossing the nuclear membrane to bind to nuclear DNA, but are incapable of
crossing the mitochondrial membrane.
A team, led by Ganesh Pandian Namasivayam, from Kyoto
University’s Institute for Integrated Cell-Material Science (iCeMS) succeeded
to re-direct PIP to cross the mitochondrial membrane so that it can access its
DNA and alter gene transcription.
They achieved this complex feat by complementing PIP with a
‘mitochondria-penetrating peptide’ (MPP), which is capable of overcoming the
mitochondria’s energy barrier. The MPP-conjugated PIP called MITO-PIP was
designed to block a specific binding site for mitochondrial transcription
factor A (TFAM). TFAM is essential in governing mitochondrial metabolism and
energy synthesis, playing a role in the transcription of a gene called ND6,
says Takuya Hidaka, the first author of the study.
The team found that a TFAM-inhibiting MITO-PIP selectively
read a mitochondrial DNA sequence and caused a 60% to 90% reduction in the
expression of ND6, depending upon the concentration used. The team then labeled
the MITO-PIPs with a molecule that fluoresces when exposed to light and, using
special microscopes, confirmed that they localized inside the mitochondria
without being present in the nuclei of treated cells.
ND6 is associated with several mitochondrial disorders,
including Leber’s hereditary optic neuropathy, which causes loss of central vision,
mitochondrial myopathy, muscle weakness, seizures and learning difficulties.
Hence, chemical control over such disease-associated genes has clinical
potential in mitochondrial gene therapy. “We plan to develop an advanced
version of MITO-PIPs that can identify and localize only inside diseased
mitochondria,” says Ganesh.
“Our proof-of-concept study provides a fresh platform that
opens new avenues for DNA-based functional ligands that are capable of altering
the mitochondrial genome in a sequence-specific manner,” concludes the
principal investigator Hiroshi Sugiyama. The study was published in the Journal
of the American Chemical Society.
http://www.kyoto-u.ac.jp/en/research/research_results/2017/170616_1.html
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