I recently attended the British Society for Research on Aging annual scientific conference which was held this year in Birmingham. There were a number of interesting talks and about 45 posters were presented. This included one from me. The details in that poster can be seen on this link.
One benefit of conferences which are in person is that conversations can continue after the presentations and issues can be refined through discussions either in the corridors or over food. The area I am particularly interested in is how the links between mitochondrial efficiency and the genome operate. I managed to refine my understanding of two of the aspects here.
The Citric Acid Bicycle
The first area I managed to refine is to understand the mechanisms that underpin citrate efflux from the mitochondria. To understand this fully it is perhaps best to consider the operation of two citric acid cycles. In fact realistically it is a Citric Acid Bicycle - as the two cycles are linked.
The normal cycle that people are used to is called variously the TCA cycle, Citric Acid Cycle or Krebs Cycle. Simplistically this can be seen as Pyruvate coming into the mitochondria and being converted to acetyl-CoA. Then that converts Oxaloacetate to Citrate, which converts to cis-Aconitate, D-isocitrate, alpha Ketoglutarate, Succinyl-CoA, succinate, fumarate, Malate and back to Oxaloacetate. It throws off various amounts of other molecules most importantly NADH, but also bringing in and getting out water.
It has been known for some time that citrate also leaves the mitochondria and this has been described such as in this paper as the non-canonical TCA cycle. This is where we get pyruvate coming into the mitochondria and being converted to acetyl-CoA. Then that converts Oxaloacetate to Citrate (as with the canonical cycle). However, at this point the cycle diverges and the citrate leaves the mitochondria via the citrate carrier. Outside the mitochondria this is converted to acetyl-CoA, then oxaloacetate and then that is converted to malate which swaps with citrate leaving the mitochondria and rejoins the main cycle and is converted to oxolacetate.
In that sense, therefore, we actually have two linked cycles. They share the process where acetyl-CoA goes to convert oxaloacetate to citrate, but then the cycles split (hence a bicycle). For citrate to leave the mitochondria it both has to take with it a single proton and swap with malate. Hence the amount of citrate leaving the mitochondria is balanced entirely with malate coming in.
Hence we can see that there are three factors that affect the rate of citrate efflux. a) The rate of pyruvate coming into the mitochondria, b) the amount of citrate carrier proteins in the mitochondrial inner membrane and c) the balance between citrate being converted to AKG or leaving the mitochondria.
To me this was particularly helpful as it clarified the link between the mitochondrial membrane potential and citrate efflux. Because the rate of citrate efflux linkes to pyruvate import and the rate of pyruvate import is controlled in part by the mitochondrial membrane potential then an increase in MMP leads to an increase in citrate efflux.
Obviously both wheels of the cycle will be going around at the same time and there is going to be a different dynamic equilibrium in each mitochondrion. However, as the MMP is essentially a measure of the ATP/O efficiency of the mitochondria it is clear why all three things are linked, ATP/O efficiency, mitochondrial membrane potential and citrate efflux.
How the Genome rides the bicycle
I also had some useful discussions about the links between acetylation and mRNA transcription. It is clear that acetylation is required to initiate the transcription of a particular gene. However, on the basis of the discussions it seems clear that the influence of acetylation is more complex once RNA Polymerase II has started transcribing. A molecular biologist I know told me previously that the acetyl transferase was dragged along with RNA Pol II to open up the histone, but it does not appear to be essential and substrate shortage may not be the cause of all of the pausing of RNA Pol II. However, acetyl-CoA is being used to acetylate other proteins and this can drive splicing processes. Hence the aggregate energy level of the mitochondria is still guiding what happens whilst a gene is being transcribed even if this process is not entirely linked to acetylation of the histone after the start of the process.
This paper, however does indicate "that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases" and that there acetylation particularly occurs at nucleosomes which are predicted to stall RNA Pol II. Hence although acetylation may not always be required it is required for certain other steps.
There remains some work to be done to understand the interplay between transcription and acetylation as the role of HDACs is not yet fully clarified. However, the mechanism whereby mitochondrial efficiency drives splicing decisions is now clear to me. For that I thank BSRA for an excellent conference.
One benefit of conferences which are in person is that conversations can continue after the presentations and issues can be refined through discussions either in the corridors or over food. The area I am particularly interested in is how the links between mitochondrial efficiency and the genome operate. I managed to refine my understanding of two of the aspects here.
The Citric Acid Bicycle
The first area I managed to refine is to understand the mechanisms that underpin citrate efflux from the mitochondria. To understand this fully it is perhaps best to consider the operation of two citric acid cycles. In fact realistically it is a Citric Acid Bicycle - as the two cycles are linked.
The normal cycle that people are used to is called variously the TCA cycle, Citric Acid Cycle or Krebs Cycle. Simplistically this can be seen as Pyruvate coming into the mitochondria and being converted to acetyl-CoA. Then that converts Oxaloacetate to Citrate, which converts to cis-Aconitate, D-isocitrate, alpha Ketoglutarate, Succinyl-CoA, succinate, fumarate, Malate and back to Oxaloacetate. It throws off various amounts of other molecules most importantly NADH, but also bringing in and getting out water.
It has been known for some time that citrate also leaves the mitochondria and this has been described such as in this paper as the non-canonical TCA cycle. This is where we get pyruvate coming into the mitochondria and being converted to acetyl-CoA. Then that converts Oxaloacetate to Citrate (as with the canonical cycle). However, at this point the cycle diverges and the citrate leaves the mitochondria via the citrate carrier. Outside the mitochondria this is converted to acetyl-CoA, then oxaloacetate and then that is converted to malate which swaps with citrate leaving the mitochondria and rejoins the main cycle and is converted to oxolacetate.
In that sense, therefore, we actually have two linked cycles. They share the process where acetyl-CoA goes to convert oxaloacetate to citrate, but then the cycles split (hence a bicycle). For citrate to leave the mitochondria it both has to take with it a single proton and swap with malate. Hence the amount of citrate leaving the mitochondria is balanced entirely with malate coming in.
Hence we can see that there are three factors that affect the rate of citrate efflux. a) The rate of pyruvate coming into the mitochondria, b) the amount of citrate carrier proteins in the mitochondrial inner membrane and c) the balance between citrate being converted to AKG or leaving the mitochondria.
To me this was particularly helpful as it clarified the link between the mitochondrial membrane potential and citrate efflux. Because the rate of citrate efflux linkes to pyruvate import and the rate of pyruvate import is controlled in part by the mitochondrial membrane potential then an increase in MMP leads to an increase in citrate efflux.
Obviously both wheels of the cycle will be going around at the same time and there is going to be a different dynamic equilibrium in each mitochondrion. However, as the MMP is essentially a measure of the ATP/O efficiency of the mitochondria it is clear why all three things are linked, ATP/O efficiency, mitochondrial membrane potential and citrate efflux.
How the Genome rides the bicycle
I also had some useful discussions about the links between acetylation and mRNA transcription. It is clear that acetylation is required to initiate the transcription of a particular gene. However, on the basis of the discussions it seems clear that the influence of acetylation is more complex once RNA Polymerase II has started transcribing. A molecular biologist I know told me previously that the acetyl transferase was dragged along with RNA Pol II to open up the histone, but it does not appear to be essential and substrate shortage may not be the cause of all of the pausing of RNA Pol II. However, acetyl-CoA is being used to acetylate other proteins and this can drive splicing processes. Hence the aggregate energy level of the mitochondria is still guiding what happens whilst a gene is being transcribed even if this process is not entirely linked to acetylation of the histone after the start of the process.
This paper, however does indicate "that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases" and that there acetylation particularly occurs at nucleosomes which are predicted to stall RNA Pol II. Hence although acetylation may not always be required it is required for certain other steps.
There remains some work to be done to understand the interplay between transcription and acetylation as the role of HDACs is not yet fully clarified. However, the mechanism whereby mitochondrial efficiency drives splicing decisions is now clear to me. For that I thank BSRA for an excellent conference.
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