Showing posts with label Yates. Show all posts
Showing posts with label Yates. Show all posts

Wednesday, July 15, 2015

362 - Mutants of Azotobacter chroococcum Defective in Hydrogenase Activity

This study isolated some hydrogenase-negative mutants of Azotobacter chroococcum by chemical mutagenesis and looked at how they behaved.

What They Saw
Almost all of the 16 mutants had almost no hydrogenase activity, as expected. Some had a little, <2% of wild-type. Some more had a little hydrogen-producing activity in the right conditions, usually less than 7% of the wild-type, but one had 40% of wild-type. That one also seemed to have a relatively active soluble hydrogenase (possibly the uptake hydrogenase in soluble form). All of them seemed able to take up nickel.

The one weirdest mutant, MCD-124, showed max activity at a different pH (5.5 instead of 8) and was weird in other ways.

Also, the authors were surprised by the frequency with which they could get hydrogenase mutants. They wondered whether the relevant genes were just more susceptible, or if the growth medium was more favorable to mutants somehow, or if there were just that many necessary genes. But judging from the genome sequence, this isn't quite a sufficient explanation.

Overall, it's hard to know exactly what's going on in this study.

Reference:
Yates, M. G. & Robson, R. L. Mutants of Azotobacter chroococcum Defective in Hydrogenase Activity. J Gen Microbiol 131, 1459–1466 (1985).

Tuesday, July 7, 2015

307 - The Relationship Between Hydrogenase and Nitrogenase in Azotobacter chroococcum: Effect of Nitrogen Sources on Hydrogenase Activity

This study looked at the influence of different sources of nitrogen on the activity of nitrogenase and hydrogenase in Azotobacter chroococcum.

What They Saw
They grew cells in batch or continuous culture with sodium nitrate, ammonium acetate or chloride, or dinitrogen gas. Cultures were either carbon- or sulfate-limited. Dissolved oxygen was kept above zero. Nitrogenase activity was measured by acetylene reduction and hydrogenase by methylene blue (or by adding H-T with radioactive tritium and measuring radioactivity of resulting water when oxygen was the electron acceptor).

There was about twice as much hydrogenase activity when cells were fixing nitrogen in batch than when they had either ammonium or nitrate. They cite other results in A. chroococcum and A. vinelandii that showed higher activity with nitrate than ammonium though, but still less than when fixing nitrogen. This might be because cells have to adapt to use nitrate, and they'll be fixing nitrogen before that happens. But care is necessary because activity changes over the course of a batch culture, increasing throughout exponential phase even when standardized by protein concentration.

In continuous cultures, they started growing with ammonium, then switched to nitrogen-free, watched what happened with hydrogenase and nitrogenase, and then pulsed a limited amount of ammonium. As expected, nitrogenase activity started up and rose to a plateau, then immediately stopped when ammonium was added, and restarted when it was removed. Hydrogenase activity showed a similar pattern, though more delayed, and it never went all the way to zero.

In sulfate-limited culture, hydrogenase activity was lower even when fixing nitrogen, about the same as with ammonium in carbon limitation, and when going from fixing to non-fixing (with ammonium), the activity declined a bit but then went back up to about the same level. Results were similar going from non-fixing to fixing. So with sulfate limitation, nitrogen source doesn't matter much.

Also with nitrogen-fixing cells in sulfate limitation, when they increased the dilution rate, hydrogenase activity decreased but nitrogenase increased. The decrease wasn't linear, though; it leveled off.

They also tested whether adding hydrogen to the atmosphere of an ammonium-grown culture would influence hydrogenase activity, and it did! Hydrogenase activity doubled. This was not the case with sulfate limitation though, only carbon limitation. They didn't test nitrogen-fixing cells.

What This Means
The continuous culture experiments helped overcome the constantly changing activity in batch cultures.

That hydrogenase activity lags behind nitrogenase activity increase when ammonium runs out could be explained by the last observation: maybe nitrogenase starts producing hydrogen (as it does) and this stimulates hydrogenase activity.

They reasoned from the data that excess carbon might inhibit hydrogenase activity somehow (like catabolite repression). I'm not sure that makes sense, but it seems possible, and does fit with the data from batch cultures, sulfate limitations, and increasing dilution rates. Interesting.

Reference:
Partridge, C. D. P., Walker, C. C., Yates, M. G. & Postgate, J. R. The Relationship Between Hydrogenase and Nitrogenase in Azotobacter chroococcum: Effect of Nitrogen Sources on Hydrogenase Activity. J Gen Microbiol 119, 313–319 (1980).

297 - The identification, characterization, sequencing and mutagenesis of the genes (hupSL) encoding the small and large subunits of the H2-uptake hydrogenase of Azotobacter chroococcum

And finally, seeming to complete our journey back in time through the discovery of hydrogenase genetics in Azotobacter chroococcum, this study looks at the structural genes, hupSL.

What They Saw
The sequences were similar to A. vinelandii's hoxKG structural genes. They tried knocking each out, then measuring hydrogen oxidation (with methylene blue) and hydrogen production (with methyl viologen). As expected, hydrogen oxidation in mutants was no higher than negative controls. Surprisingly, they did see hydrogen production in the some of the different mutants with a strong electron donor, but it was less than in the wild-type. Only the mutant with an insertion very close to the start of the hupS gene had no hydrogen production.

What This Means
It seems like a fragment of HupS is sufficient to produce hydrogen with a strong electron donor, but not as much as with both HupS and HupL completely intact.

Reference:

Monday, July 6, 2015

295 - Sequences, organization and analysis of the hupZMNOQRTV genes from the Azotobacter chroococcum hydrogenase gene cluster

This study focuses on the hydrogenase genes in Azotobacter chroococcum. They had already found hupSL encoding the structural genes (equivalent to A. vinelandii's hoxKG I guess), and then the accessory genes hupABYCDE further downstream (homologous to A. vinelandii's hypABFCDE). Now, in between, are the hupZMNOQRTV genes, completing the 16-gene operon.

What They Saw
This set of genes seems to be homologous to A. vinelandii's hoxZMLOQRTV string, making the whole operon very similar in both organisms.

As in previous studies, HupZ (and its analog, HoxZ) seems to be an electron carrier in the membrane, possibly a cytochrome. When they knocked it out, they observed similar results to 070: hydrogenase could oxidize hydrogen with methylene blue as an electron acceptor, but not with oxygen, so HupZ seems to be part of the transport chain to oxygen.

Based on comparison with homologs in other organisms, HupM may help the hydrogenase attach to the membrane, or with processing the subunits. It's unclear. The other genes may be involved in processing or metal stuff. HupR may be another electron-carrying protein. Further study is required.

Reference:
Du, L., Tibelius, K. H., Souza, E. M., Garg, R. P. & Yates, M. G. Sequences, organization and analysis of the hupZMNOQRTV genes from the Azotobacter chroococcum hydrogenase gene cluster. Journal of Molecular Biology 243, 549–557 (1994).

Tuesday, June 30, 2015

159 - Effect of chelating agents on hydrogenase in Azotobacter chroococcum: Evidence that nickel is required for hydrogenase synthesis

This study used chelating (metal-binding) compounds to study the cofactor of hydrogenase in Azotobacter chroococcum.

What They Saw
All the chelators they added (NTA, EDTA, etc.) decreased the hydrogenase activity in batch cultures, though to different extents. NTA was much stronger than EDTA. The effect was not inhibition of already-formed enzyme (since adding chelators to resting cells or extracts didn't affect activity), so it must be from preventing formation of additional enzyme.

They tried adding trace metal salts along with the chelators to see if pure excess of whatever was missing could restore activity. Copper, zinc, and manganese didn't really do anything. Cobalt helped if it was added in fairly large amounts, but the most helpful was nickel. Adding extra iron boosted this effect even more.

Monitoring nickel uptake by adding radioactive nickel, they saw that cyanide completely wiped out uptake (possibly by binding the nickel), but juglone and 2,4-dinitrophenol enhanced it (despite inhibiting respiration). Sodium azide didn't really affect either. The chelators they tested earlier generally seemed to inhibit nickel uptake too, generally in the same proportions as they had inhibited hydrogenase activity.

What This Means
Chelators seem to inhibit hydrogenase, but rather than acting on the enzyme directly, it seems to be by inhibiting its synthesis, and even this mechanism seems to be by inhibiting nickel uptake in most cases, rather than something more direct. Nickel is important for synthesizing the enzyme; it's a part of its essential cofactor. It seems like cobalt might be able to substitute for nickel somewhat though. I wonder if palladium would work too, since it has similar orbital arrangements. But apparently cobalt doesn't help in the absence of chelators or contaminating trace metals, so maybe it only helped here because it distracted the chelators away from nickel (so to speak).

Reference:

Tuesday, April 28, 2015

113 - The hydrogen cycle in nitrogen-fixing Azotobacter chroococcum

Azotobacter chroococcum makes hydrogen when fixing nitrogen, but its uptake hydrogenase reoxidizes hydrogen. It wasn't clear what the purpose of this reoxidation is, or in what conditions it's useful, or how much hydrogen is produced in different conditions, so this study aimed to find out.

What They Saw
When they had bacteria in carbon-free broth, with hydrogen present in the atmosphere, the bacteria were able to reduce acetylene with nitrogenase using only energy from the hydrogen. No such activity was observed without hydrogen present. Even when mannitol was added up to 2 g/L, adding hydrogen still increased the acetylene reduction activity, though the proportion of activity attributable to hydrogen decreased as mannitol increased, though surprisingly it leveled off above zero even when mannitol wasn't the limiting nutrient anymore; it's possible that electron transfer from hydrogen works differently.

They also tried increasing oxygen levels with a little mannitol; when hydrogen was absent, oxygen became inhibitory about twice as fast as when hydrogen was present, so hydrogenase seems to help protect the nitrogenase. The effect went down to around zero as mannitol increased though.

They looked at hydrogen production when fixing nitrogen with various limitations (carbon, nitrogen, oxygen) in continuous culture; unlike in batch culture, cells seemed to evolve significant hydrogen. They compared hydrogen produced in air to that produced when replacing air with argon to get the proportion of nitrogenase activity going to hydrogen (presumably in air, the remainder goes to actually fixing nitrogen), and found that under oxygen or nitrogen limitation (whatever that means here), the proportion was 40-50% going to hydrogen. In carbon limitation, it was lower, around 13%, but they said that hydrogenase activity was higher in this case (for some reason) so it doesn't represent the true proportion (since not all hydrogen is observed).

What This Means
Since hydrogen could protect nitrogenase from oxygen, it seems like its electrons go to oxygen through the respiratory chain rather than to power nitrogenase activity.

It is somewhat puzzling that the hydrogenase would work so well when acetylene is present, since acetylene has been shown to inhibit the hydrogenase (112). They observed that in this study too. So it's possible that the hydrogenase might be even more useful when acetylene is not present. But 40% acetylene is required to completely inactivate hydrogenase, whereas they only used 8% in the activity assays.

40-50% electron flux going to hydrogen is higher than estimated by others, at least for the molybdenum nitrogenase, but it's unclear the effect of the limitations imposed.

Here's the model they propose:
Walker and Yates, 1978
Reference:
Walker, C. C. & Yates, M. G. The hydrogen cycle in nitrogen-fixing Azotobacter chroococcum. Biochimie 60, 225–231 (1978).

Monday, April 27, 2015

108 - The Beneficial Effect of Hydrogenase in Azotobacter chroococcum Under Nitrogen-Fixing, Carbon-Limiting Conditions in Continuous and Batch Cultures

Since hydrogen is an energy-rich gas, and nitrogenase produces hydrogen, one would expect that diazotrophs that can re-oxidize the hydrogen they produce (using uptake hydrogenases) would have a competitive advantage over those that lack an uptake hydrogenase. However, results of previous studies of this question, in this and other organisms, have been mixed (019,065).

This study is another comparison of Azotobacter chroococcum strains, one with and three without an uptake hydrogenase, in a variety of conditions.

What They Saw
As the dilution rate increased in carbon-limited nitrogen-fixing conditions, the wild-type strain's growth yield remained relatively constant, while the three mutants' yields were noticeably lower at most rates. There was no noticeable difference when fixed nitrogen was provided. When oxygen or sulfate were limiting, there didn't seem to be much difference between strains.

When the strains were mixed together in equal densities in continuous culture, the mutants seem to overtake the wild-type a couple times at lower dilution rates, but the wild-type always took over at higher rates. With ammonium added, there was no consistent pattern.

What This Means
The mutants in this study were obtained by random mutagenesis, so the lack of hydrogenase wasn't necessarily the only difference from wild-type. Still, the three strains seemed to give some fairly consistent results.

The advantage seen in the wild-type occurred in low-density populations or high dilution rates, so it seems like the hydrogenase helps recover energy (or protect nitrogenase from oxygen) rather than preventing inhibition by hydrogen itself.


Reference:
Aguilar, O. M., Yates, M. G. & Postgate, J. R. The Beneficial Effect of Hydrogenase in Azotobacter chroococcum Under Nitrogen-Fixing, Carbon-Limiting Conditions in Continuous and Batch Cultures. J. Gen. Microbiol. 131, 3141–3145 (1985).

Monday, April 20, 2015

112 - The Effect of Nutrient Limitation on Hydrogen Production by Nitrogenase in Continuous Cultures of Azotobacter chroococcum

That nitrogenase produces hydrogen gas had been known for a while; this study wanted to see how different nutrient limitations affected this phenomenon.

They grew Azotobacter chroococcum on mannitol B medium in continuous culture, with limitations in carbon, sulfate, oxygen, or dinitrogen. Then they measured acetylene reduction, hydrogen production, and oxygen consumption in vivo and the former two on purified nitrogenase. Also update hydrogenase activity directly.

What They Saw
There was very little hydrogen evolved by oxygen-limited cultures in air, unless the uptake hydrogenase was inhibited by acetylene first. Replacing air with an argon/oxygen/CO2 mix (without nitrogen) also increased hydrogen evolution to a similar level. With both treatments, the hydrogen seen was much higher.

When limited in sulfate, the hydrogen produced under air (with hydrogenase active) or under argon mix seemed much higher (at least proportional to the amount of protein in cells).

Under argon mixes with different proportions of oxygen, hydrogen evolution seemed highest around 10% oxygen. With nitrogen instead of argon, the peak was similar. Too much or too little oxygen was not good. And despite the high amount of hydrogen, around 10% (actually between 6-12%) was when the most nitrogen was being fixed too, such that the ratio of hydrogen produced to nitrogen fixed was as low as 1 (or 0.5, when sulfate-limited).

In carbon-limited cultures, though, the optimum oxygen value was 3%, though oxygen consumption increased as oxygen increased, at least up to 6%.

In vitro, the hydrogen-nitrogen ratio increased as the ratio of dinitrogenase to dinitrogenase reductase increased, though higher levels of ATP decreased this effect. Sulfate limitation didn't really affect this finding.

What This Means
This makes sense; some oxygen is required to generate ATP to power the nitrogenase, but too much oxygen requires extra carbon to detoxify it, so there's less energy for nitrogenase.

It seems like a lack of dinitrogenase reductase or ATP reduces the ability to fix nitrogen instead of just producing hydrogen. I wonder if dinitrogenase has any effect on its own in the absence of ATP or its other component.

Chemically it's unclear how or why nitrogenase produces hydrogen, but it seems to be an essential part of the nitrogen fixation process.

Reference:
Walker, C. C., Partridge, C. D. P. & Yates, M. G. The Effect of Nutrient Limitation on Hydrogen Production by Nitrogenase in Continuous Cultures of Azotobacter chroococcum. J. Gen. Microbiol. 124, 317–327 (1981).

Monday, October 14, 2013

019 - The Effect of Nutrient Limitation on the Competition between an H2-uptake Hydrogenase Positive (Hup+) Recombinant Strain of Azotobacter chroococcum and the Hup- Mutant Parent in Mixed Populations

Since Azotobacter has this uptake hydrogenase enzyme that seems to recover the energy lost as hydrogen gas from nitrogen fixation, it is worth testing to see if this hydrogenase actually does provide a benefit to the bacteria. This study was done in A. chroococcum, not A. vinelandii, but they're related enough that we should be able to generalize the data gathered, with caution.

The hydrogenase works by taking H2's electrons and passing them through the electron transport chain to oxygen to generate a membrane potential (like voltage) that provides energy for the production of ATP (the cell's energy currency, that it uses to power many of its reactions). This can be an important process for crop production, since some crops (legumes) are colonized with bacteria that fix nitrogen for them, but at the time it was unclear whether the uptake hydrogenase in this system was actually helpful for the crop at all. So the authors decided to study the question in an easier system: free-living Azotobacter.

In this study, the strains under investigation were a mutant strain, offspring of the wild-type, that lacked hydrogenase, called MCD103; and another strain derived from MCD103, called MCD503, that did have a hydrogenase because they crossed MCD103 with a plasmid containing wild-type hydrogenase genes, resulting in MCD503, which was the same as MCD103 in every way except the hydrogenase (presumably).

These strains were grown together in continuous culture/chemostats, fixing nitrogen. If one had a growth advantage over the other, it would come to dominate the culture in time. They measured proportions of the strains in two ways: first, by plating them out on agar and using a technique called "scrying" (which seemed to consist of exposing the colonies to H2 in a sealed box with an indicator present, such that those that had hydrogenase would stay white and those that didn't would turn blue-black) and then counting the colonies of each kind. Second, by plating and transferring individual colonies to a 96-well plate, then exposing all of them to radioactive hydrogen (tritium, 3H2) and measuring which ones retained radioactivity (indicative of consuming the hydrogen with their hydrogenase). These sound like rather painful and burdensome procedures; nowadays people would probably just do gene sequencing or transcript analysis to see how many copies of hydrogenase genes/transcripts were present over time. I suppose the techniques in this paper may give a more direct measure though.

So anyway, about what they found. When sucrose (sugar) was the limiting nutrient (that is, when the cells were consuming all the sugar they were given and could've consumed even more), the hydrogenase-positive strain MCD503 came to dominate the culture over time, regardless of the proportions of the strains at the beginning of the experiment. Even when initially there were 99 hydrogenase-negative cells for every one hydrogenase-positive cell, before too long they saw the amount of hydrogen produced falling quickly as hydrogenase activity increased. The domination happened faster at higher dilution rates, which makes sense because faster-growing cells would be able to tolerate these better. When fixed nitrogen (ammonium) was added to the cultures, neither strain dominated the other consistently. So it seems that hydrogenase is important when fixing nitrogen.

When nutrients other than sucrose were limiting, though, the situation was not always the same. When phosphate was limiting, MCD503 still dominated, though not as well as with sucrose limitation. However, when oxygen was limiting, the strain missing its hydrogenase (MCD103) was dominant! Even when MCD503 started as 78% of the cells present, it fell to less than 20% before stabilizing. So it seems that hydrogenase-negative strains can deal with low oxygen better.

When sulfate was limiting, MCD503 declined slowly, but it declined more quickly when iron was limiting (makes some sense because the hydrogenase requires iron in its cofactor).

It was interesting to note, also, that MCD503 (hydrogenase-positive) consumed its own hydrogen but also that produced by MCD103 (hydrogenase-negative). Might've contributed to its faster growth in some conditions, and this is consistent with how the domination slows down as more and more of the population is MCD503 (thus there is less hydrogen produced by its competitor to steal).

Speculations about explanations for the findings, as far as I understand them: carbon-limiting results make sense because H2 oxidation adds to the energy recovery and makes up for some of the limitation.
Phosphate-limiting results make sense because hydrogen could help increase consumption of oxygen to protect nitrogenase and hydrogenase, which are sensitive to it.
Oxygen-limiting results make sense because hydrogen oxidation might take precedence over other kinds in the electron transport chain due to greater affinity.
And sulfate- and iron-limiting results make sense because hydrogenase requires sulfur in addition to iron, so the cells would devote some of their nutrients to this enzyme instead of other, more important ones; while hydrogenase-negative strains wouldn't have this disadvantage.

So it seems that the hydrogenase is helpful in some circumstances and harmful in others. Interesting results.