When brine shrimp release their eggs into Utah's salty lakes, it could take the tiny embryos another four years, before they finally hatch into the next generation. But the delay is not because the shrimps have the longest gestation period on earth, the tiny crustaceans have evolved the ability to switch into a state of suspended animation if their environment turns against them. Steve Hand explains that if the waters become hypoxic, or an embryo finds itself buried under layers of decomposing silt, the embryo depresses its metabolism to deathly low levels in a bid to conserve valuable energy resources until conditions improve. How the embryo choreographs each metabolic system's shut down has fascinated Hand for years. Having analysed how they downregulate the translation of protein molecules throughout each cell, he has turned his attention to transcription in the embryos' mitochondria, and found that they coordinate shutting down their transcriptional machinery in part by dropping the cell's pH (p. 577).
Compared to protein synthesis, which consumes almost half of the cell's energy budget, RNA transcription is relatively inexpensive, consuming only one tenth of the cell's valuable ATP supplies. But the embryos cannot bear even the tiniest energetic cost if they are to survive years without oxygen. Hand knew that as the embryo's metabolism slowed, the cell's pH fell dramatically from 7.9 to 6.4 and nuclear transcription ceased, but would transcription also cease in the cell's mitochondria in response to a lower pH?
Hand and his team travelled to the salt lakes of Utah to gather thousands of the dormant embryos as they bobbed to the lake's surface during spawning. Back in the lab, they extracted mitochondria and simulated the low pH conditions in the cell as the oxygen levels fell; the transcription rate dropped by 90%! Was it simply the lack of oxygen or the acidic conditions that was slowing the mitochondria's production of RNA? Hand's colleague, Brian Eads, tested the mitochondria's transcription rates as he lowered first the pH and then the oxygen levels. The transcription rates fell under both conditions: acidification of the cell must be coordinating transcriptional down regulation in both the nucleus and the mitochondria.
Having found that this enormous pH drop signals several organelles to cut transcription, Hand and Eads wondered what was different about the mitochondria's transcriptional machinery at both pHs. Was the polymerase enzyme that synthesises the RNA message failing to bind the DNA, or had the pH shift destroyed the enzyme's activity? They measured transcriptional initiation and found that it decreased at low pH.
Not knowing why initiation fell, they wondered if the drop was due to decreased polymerase binding to the DNA. The polymerase enzyme can only bind DNA if the correct pattern of transcription factors is already in situ. They looked at the patterns of proteins bound to the DNA at low and high pH to see if the lower pH had altered the pattern of DNA bound transcription factors. But the patterns were identical! Hand admits that he was surprised by this result, but he adds that many transcription factors only function if they've been modified by addition of a phosphate molecule. He suspects that the pH change could have disrupted RNA transcription by interfering with the protein modification.
