Comments
Annonymous wrote:
Hadi:
Is it not
possible to use your substrate function for both light and CO2?
09/05/04 13:03:38
hadi wrote:
The simple
answer is no. Based on the theory, the concept of rate determining step
suggests that in a multi-step reaction only the slowest step determines the
rate of reaction. Therefore only one enzyme-substrate complex can be limiting.
This means that either a single substrate can be limiting or the enzyme.
09/08/04 09:42:23
hadi wrote:
Based on my
previous comment, a modification is necessary in the abstract in:
1)
Consideration of two steps for the reaction, one for each
"substrate".
The word
"substrate" should be changed to "enzyme-substrate
complex".
H.F.
09/16/04 16:40:27
hadi wrote:
I have
received a number of interesting and thoughtful comments by email from some
distinguished scholars with specific interests in activation and biochemical
reaction of Rubisco. To the extent that it is beneficial to the readers, and
protects the anonymity of the commentators, I would provide the comments and my
answers gradually in the following paragraphs.
09/17/04 12:54:57
Comment Series 1: wrote:
A model based
only on rubisco parameters is certainly a valid approach, but measurement of
many of the required parameters is difficult - RuBP, PGA (for product inhibition
that your model seems to use), inhibition constants, etc.
09/17/04 13:25:41
hadi wrote:
Answer: From
equations 35 and 36 of the model, you may note that RuBP regeneration is
considered to be either “energy-limited” or “Calvin cycle capacity-limited”. In
either case RuBP is replaced with its equivalent energy. Therefore,
measurements of RuBP concentration are not required. Simulations of Fig 3a give
examples of “energy-Limited” cases of RuBP regeneration, and all the parameters
of model are calculated on the basis of measurements of initial conditions and
maximum saturation velocities. No other intermediate value or any empirical
constant is needed for the model.
Extra
measurements of values near light saturation are needed for CO2 saturated
carboxylation to establish possible limitations of Calvin cycle capacity on
Vmax as shown in Fig. 2a.
It is
important to note that, often our judgment of saturation may differ
significantly from what the plants tell us. For example, the two-system theory
of Farquhar et al assumes that, Rubisco is always saturated with RuBP, and
ambient CO2 is sufficient to saturate Rubisco. Therefore, any deviation of A/Ci
curve from Michaelis Menten curve in mid-day hours should be due to a
limitation in RuBP regeneration of Calvin cycle. Thus, when Price et al (1995,
Fig 6a), find a value of A = approx. 24 (see units) at Ci = 800, the limitation
is considered due to inadequate RuBP regeneration from Calvin cycle, while CO2
and light are saturating. Yet, in the same paper, (Fig 8a) a much higher value
for A of about 60, at external CO2 of 1750 is reported by the same authors and
for the same plants. This rejects the saturation of CO2 for the first case (i.e
for A=24). A similar Amax value of about 60, had also been previously reported
by Masle et al (1993) for the same plants, that rejects an accidental one time
error for the latter data.
09/19/04 23:06:39
comment series two: wrote:
I think the
success of the Farquhar et al model is that the model parameters can be easily
determined by various experimental methods for validation analysis. In your
model you have sufficient parameters to "fit" or simulate any
photosynthetic response curve but it is not obvious (to me at least) what sorts
of measurements one would make to independently verify the values of the model
parameters you obtain.
09/24/04 10:42:13
hadi wrote:
My best
interpretation of this comment is that, I have not been clear enough in my
presentation of the model and its comparison with that of Farquhar et al.
I still leave
the full comparison to be made by other modelers and model users. But, briefly,
there are several versions of the two-system model of Farquhar et al; such as,
the integrated 1980 model, de Pury & Farquhar (1997) for the response to
light, integrated model of von Caemmerer (2000), and a few others. There are at
least two empirical parameters in these models, Jmax and the convexity factor.
The convexity factor is a coefficient that varies widely (Evans & Farquhar
1991, Ogren & Evans 1993, Ogren 1993) and according to Collatz et al
(1990), it has no mechanistic meaning. There are no such parameters in my
single-enzyme model. As mentioned under the “General Discussion”, if “V2”
and its coefficient are excluded from equation 47, the remaining part shows the
kinetics of an equilibrium reaction; a1+a2 determine the magnitude of enzyme
substrate complexes including the feedbacks relative to the last step, while “V2”
and its coefficients reflect the effect of Rate-Determining Steps and the
irreversible link between the two steps. With all such details, yet there is no
parameter in the model that requires additional effort in the measurements
compared to Farquhar et al model. Indeed, the model reduces the number of
parameters to be measured by establishing their internal relationship. For
example, Ogren & Evans (1993) use three individual response curves, with
more than three parameters for each, to describe a set of data for eucalyptus
that could be described more elegantly and accurately, with fewer parameters as
shown in Fig 3.
09/27/04 11:06:50
Comments series three
wrote:
As best I can
determine, neither the Farquhar et al. model or your model explicitly uses
Rubisco activation state as a variable. This is one parameter that can be
easily measured and ,....... Of course the downside is that the dependence of
Rubisco activation state on many of the other parameters that one might like to
have in a model are not always well known.
10/01/04 14:17:09
hadi wrote:
Answer: Well,
as far as my model is concerned you are right. I do not use the term
"Rubisco activation state" explicitly, because it may be interpreted
very broadly, and out of the scope of this work. However, what I have said
explicitly, and have used in my derivation of the model mathematically, (eqns
19 and 20), is that the Kcat of the reaction varies for different velocities.
This is a quality distinctly different from that of Michaelis-Menten type
models.
10/02/04 21:27:03
steve wrote:
Is your model
based on product or feedback inhibition as mentioned in comment series 1?
10/28/04 11:26:52
hadi wrote:
A very good
question. The answer is not a simple Yes or No. Let us look back at Fig. 2
first. Take the simulation for spinach; we have three curves, one shows the
initial maximum reaction. This shows the maximum possible rate of reaction,
when CO2 is not limiting; it varies with light, it is transitional and is
limited by the Maximum Rubisco Capacity (Vcmax). This is consistent with the
potential transitional carboxylation rate that Laisk (1985) and Ruuska et al
(1988) have experimentally found and von Caemmerer (2000) is using in her
calculations. The second curve gives the actual steady state rate of
carboxylation when energy is limiting, and it seems to be equivalent to what is
often considered as Rubisco activation state when CO2 is not limiting. This
varies for different levels of carboxylation and its maximum is determined by
the Rubisco activation state at light saturation (Vmax). Therefore, the
limitation of the first step is certainly not due to feedback or product
inhibition. For the lack of a better term, I would call it conformation
inhibition, because I think it is mainly due to conformation of enzyme-RuBP
complex and the ping-pong mechanism of Enol-RuBP. However, a side chain inhibition
by xylulose-1,5 bisphosphate (McCurry, S.D., and Tolbert, N.E. 1977, J.Biol.
Chem. 10:252:23:8344-6.) may have the same effect and can lend additional
strength to this inhibition. The third curve shows the limitation of the second
step. When CO2 is saturating, it reflects the other possible inhibitory factors
in the second step, such as the effect of feedback or product inhibition by
PGA. Therefore, when CO2 is limiting, such as in the cases given by Price et al
(1995, Fig 6a & Fig. 9a), a consideration of a limitation in RuBP
regeneration system cannot be supported logically and experimentally, as
evidenced by Fig 8a of the same authors.
Therefore, at
"Light Saturation" , when there is no response to CO2, the
possibility of other limitations such as feedback inhibition by Calvin cycle
metabolites can be explored.
10/29/04 17:15:00
Peter wrote:
I like your
model. It seems to work well; however, it is not clear to me how you can
explain the role of Rubisco activase here.
11/04/04 13:32:13
hadi wrote:
Thak you
Peter. Rubisco activase is effective for enzyme activation-deactivation. This
model starts on the assumption of full activation at first, and introduces the
factors that cause de-activation through holding the enzyme in the forms which
are not readily productive. Because of this assumption, the content of Rubisco
activase and its contribution to the rate of reaction do not enter into the
model directly.
11/08/04 15:27:00
Mark. wrote:
Hadi:
The model of
Farquhar et al is known as Rubisco limited model. This name is used in the
literature and is accepted by von Caemmerer 2000. Is there any good reason for
the change of name to Two-Limitation model?
Mark.
11/12/04 08:01:13
hadi wrote:
Hi Mark;
Thank you for
your question. The fact is that, except for the paper of Carl Bernacchi and his
colleagues (Plant Cell & Environ 2001, 24:253-9), I have not come across
such references. What I mave most commonly observed has been
"Rubisco-limited photosynthesis" for the steep part of the CO2
response curve as opposed to "RuBP limited photosynthesis" for the
plateau of the curve. I did not find a reference to "Rubisco-Limited model"
in von Caemmerer 2000. If such name, or any other name is preferred by the
model developers I would certainly use it. The term "two-limitation"
model was used for the lack of a better name, and was proposed by one of the
prominent contributors to the Farquhar et al school of thought.
11/12/04 23:48:55
Peter wrote:
Hello again
Hadi:
Correct me if
I am wrong please. The difference between your Step 1 and Step 2 models is
that, if a1=0 then model 1 will be changed to Michaelis Menten equation, while
if a2=0, the model for step 2 will not change. Is this a correct
interpretation?
11/25/04 02:02:00
hadi wrote:
Hello Peter.
This is a very good question. If a1=0 then you are mathematically correct.
However, biochemically, when step 1 is limiting, a1 =k9/k3 should be larger
than 1+a2, therefore, it cannot be equal to zero. Because of this, when a1 and
a2 are at their minimum values (a1=1, a2=0), the minimum value for “a” in
equation 40 is 0.5 as shown in equation 43. In single-substrate Michaelis
Menten model, the physical phase of random collision between the substrate and
enzyme is assumed to be much slower than the biochemical phase of product
formation and release. Because of this, it is possible to assume that the
amount of enzyme engaged in the biochemical phase is negligible relative to the
total concentration of enzyme. However, in two-substrate ordered reactions,
there are two such combined steps. Although, due to Rate-Determining Step, we
consider a single substrate equation for the limitation of the slower step, we
cannot totally ignore the enzyme that is engaged with the faster step,
particularly when enzyme becomes a limiting factor. Therefor, in general,
two-substrate ordered reactions, such as carboxylation or oxygenation do not
follow Michaelis-Menten type models for steady state conditions.
11/25/04 10:35:24
Stan wrote:
Hadi:
Can you
compare your model with Rubisco model of Mott & Woodrow?
12/11/04 12:16:13
hadi wrote:
Hi Stan: Two
different directions; Mott & Woodrow start with Rubisco activation and go
through the transitional reaction rate to come to carboxylation. I start with
activated enzyme and model the carboxylation. I intend to add a component also
for enzyme activation, although it does not materially change the model.
Perhaps a comparison can be more meaningful after that.
thanks
anyway.
12/11/04 12:47:08
Rob wrote:
Hi
I am a grad
student and a bit mixed in who says what. is this correct?
Farquhar et
al: steep part of the response to CO2 is rubisco limited and the phateau RuBP
regeneration limited.
Farazdaghi:steep part of the same curve CO2 limited, and the
plateau enzyme?
12/11/04 13:28:47
hadi wrote:
Hi Rob:
You are
correct in both cases.
In the case
of my work, two response curves are needed for complete analysis: One curve for
response to CO2 at RuBP (represented by radiation) saturation, and another
curve for the response to RuBP at CO2 saturation. With such curves the plateau
is always limited by Rubisco enzyme, either directly through co-limitation of
enzyme-substrate complexes of the two substrates, or indirectly through side
chains (eg xylulose bisphosphate, ...) or feedback inhibition by PGA.
12/16/04 08:17:10
Nick wrote:
Sir:
According to
your theory the initial rate of carboxylation follows Michaelis-Menten
equation. Does it not mean that Michaelis-Menten controls the activated level
of Rubisco too?
Nick.
12/29/04 12:10:13
hadi wrote:
Thank you for
the question Nick.
Yes it does,
but for the tramsitional rate only when the total enzyme participates in
production of the maximum rate of reaction (Vcmax). But, under steady state
conditions, the enzyme-substrate complex of the slower step limits the rate of
release of free enzyme upon which Vcmax is dependent.
01/02/05 01:49:33
Jerry wrote:
It is interesting
that the approximate versions of your model for light and CO2 turn into
Blackman type equations with or without the convexity factor respectively. Can
you elaborate on the differences of your model under these conditions with the
Blackman or Farquhar et al model please?
Thanks;
Jerry
01/21/05 10:34:27
hadi wrote:
Thank you for
your question Jerry. Indeed, equations 43 and 44 are the Blackman look alike
equations; the coefficients are approximations that are difficult to trace back
to their origins without knowledge of their history and the assumptions made
for their derivations. The use of such models cannot be encouraged, except for
use as a preliminary guideline when one knows the limits of the application. As
an example about the limits of validity, I have given equation 46 as a close
approximation of net photosynthesis from rectangular hyperbola for the
transitional step. For this purpose, I think the equation can provide reliable
outputs. But for equations 43 and 44 the degree of approximation particularly
with respect to the limits and extent of interactions is not clear at this
stage. This is because the coefficients that are omitted or approximated in
equations 40, 41 and 42 are related to the distribution of enzyme between the
limiting “enzyme form” (rate-determining step) and the rest of the enzyme for
which we do not have complete information. Further work on these coefficients
can help scientists to a better understanding of the origins of the
inefficiencies of Rubisco, and perhaps to a better design for enzyme.
The next
part, about a comparison with the model of Farquhar et al, this has also come
up in some private communications, Originally, I thought that I had given my
views in brief and my preference was that other interested researchers and
scholars pursue the subject matter. However, I may have to expand the subject
matter further myself.
01/27/05 13:25:36
Jerry wrote:
Hi, Thank you
for your response. However, you mentioned that the "rate-determining
step" (RDS) is dependent on the limiting "enzyme form". In other
references, RDS is said to be related to either Calvin cycle or Rubisco. Would
you comment on the differences please? Thanks.
02/11/05 12:04:45
hadi wrote:
Jerry:
Thank you for
your question and comments.
I have used
the term “rate-determining step” only for the limiting component of the
velocity of reaction within the boundaries of one enzyme. I preferred the use
of the term “enzyme form” over “substrate” limitation, in order to keep the
reader conscious that the enzyme is also a component, that is associated with
the limiting factor and may cause feedback and limitation for other components.
In a chain of
multi-substrate, multi-enzyme (a multi-currency system) such as Calvin cycle,
the analysis of system can be made for the segments (subsystems) that can be
secured for identification of their inputs and outputs. Calvin cycle, representing
the dark reaction, can be divided into a few subsystems for analysis, which
include Rubisco, triose-phosphate pathway, and RuBP regeneration pathway.
However, sometimes the subject is a comparison of Rubisco and Calvin cycle, in
that case Calvin cycle could include both triose-phosphate and RuBP
regeneration pathways. Therefore, it is difficult to decide who or what model
is right without going into the specifics of the subject matter.
02/23/05 16:15:24
Nico wrote:
Have you
published your article in any journal? In case I would want to include it in an
article on coffee photosynthesis I’m currently writing .
02/24/05 11:15:57
hadi wrote:
Nico:
Thank you for
your interest. Internet publications are treated in the same way as conference
papers. therefore you can refer to the paper as:
Farazdaghi,
Hadi (2004) A theory ....
good luck
with your article
02/26/05 11:22:57
hadi wrote:
Because of
the increase in the length of the questions and comments section, longer
discussions are removed, and will be included in the articles that are planned
for future dates, one on Rubisco activation state and the other on the
limitations of the biochemical theory and the two components of the model of
Farquhar, von Caemmerer and Berry (1980), von Caemmerer and Farquhar (1981).
Other questions and comments will be welcomed.
06/19/05 02:17:46
hadi wrote:
I have
received a considerable number of emails to return the comments and remove them
only after my review of Farquhar et al model is posted. So, I will do
accordingly.
The question
of steve I have described, but the question of Hugh was my critique of the
model of Farquhar et al. His comment was that if it were that simple, how come
no body noticed that in the past 25 years?
06/23/05 23:39:21
hadi wrote:
A reader had
asked about the Rubisco-limited models and the difference, if any, between the
definition of Rubisco limitation between the two models of Mott & Woodrow,
and Farquhar et al. Unfortunately, by some error, the actual question of the
reader is deleted. With apologies to this reader that the exact wording of the
question is not kept, the answer is given below:
Hi Steve-
Thank you for
your comment and question.
Indeed, you
are correct, there is a world of difference between the two Rubisco-limited
definitions in modeling photosynthesis. The differences are based on what the
models represent. Mott & Woodrow’s Rubisco limitation represents the activation
of Rubisco by Rubisco activase and radiation, which influences both Rubisco
activity and RuBP regeneration through Calvin cycle.
This is
meaningful theoretically and defendable experimentally, but most importantly,
contrary to the Rubisco-limited assumptions of Farquhar et al, their conclusion
is enzyme-specific and limited only to Rubisco. They do not make
generalizations that may extend to other enzymes.
Farquhar et
al (1980) consider a fully activated RuBP saturated Rubisco, and assume that its
reaction rate, is Rubisco-limited at low P(CO2). Well, this is their assumption
for fully activated Rubisco and it is possible to debate the validity of this
assumption.
But the
problem gains a universal dimension when von Caemmerer & Farquhar (1981) calculate
the derivative of the Michaelis-Menten equation. They use high school
mathematics to show that initial slope is correlated to Vcmax.
The authors
present this relationship as a mathematical proof for validation of their
theory that carboxylation rate is limited by Rubisco because the initial slope
is Rubisco-limited.
This is
contrary to the fact that the rate of carboxylation is correlated with CO2, and
therefore, according to both Blackman and Michaelis-Menten models,
carboxylation rate must be CO2 limited.
The
mathematical interpretation of von Caemmerer and Farquhar defies the basic
principles of mathematics. This apparently seems to be immaterial to these
modelers, as Collatz, Berry, Farquhar and Pierce (1990) in response to the
previous version of this model by Farazdaghi & Edwards (1988) state:
“This model
(Farquhar et al) is based on a framework of assumptions rather a rigid
mathematical formulation like the” Farazdaghi & Edwards model.”
The
mathematical interpretation of von Caemmerer & Farquhar (1981) is uniquely
incorrect. If it were correct, all the reactions with fully activated enzymes
that follow Michaelis-Menten kinetics must have been declared enzyme-limited at
their lowest substrate concentration. So, it means that all fully activated
Michaelis-Menten reactions will have to be most severely substrate-limited.
I intend to
provide a broader review of this model in future months.
06/23/05 23:42:42
hadi wrote:
Hi Hugh:
Thank you for
your question.
The theory of
Farquhar et al looks very simple and “at first sight” is very convincing. It is
not possible to talk critically about a model that is widely used without
hurting some model users. However, any incomplete discussion would not be
helpful to the model users either. In the past, criticisms have been brushed
off with some fine, seemingly scientific, maneuver. If the past can be a lesson
for the future, what is that lesson?
The problem
of the model users is not that simple. Many do not have the mathematical
background to examine the fundamentals of a model. The criteria for judging a
model for some of these model users is faith on the authority of the modelers,
particularly if this criteria is combined with two magic words: “it fits” or
“it works”. This is exactly what the architects of this widely used model have
been preaching. Collatz, Berry, Farquhar & Pierce (1990) in review of the
previous version of our model (Farazdaghi & Edward 1988) and promotion of
the model of Farquhar et al, emphasize that their model works, though with the
help of an empirical convexity factor. They recommend that: Do not fix
something that works. There is apparently no attention to “how it works” or
“why it works”.
But, in
fairness to the model users, it may be difficult to note the delicate
value-exchanges in the abstract of von Caemmerer and Farquhar (1981) in which
from statement #1, statement #2 is concluded:
1.-"...the initial slope of the response of CO2
assimilation rate to intercellular p(CO2) could be correlated to in vitro
measurements of RuP2 carboxylase activity….”
2.-"…These results are consistent with the hypothesis
that CO2 assimilation rate is limited by the RuP2 saturated rate of the RuP2
carboxylase oxygenase at low intercellular p(CO2)...".
Simple
language translation: 1- the initial slope is proportional to Rubisco activity
(this is an incorrect statement, based on equation A16, initial slope is
proportional to Vcmax).
In statement
2, they conclude that, CO2 assimilation rate at low CO2 is limited by Rubisco.
This statement is incorrect, based on either the original or corrected versions
of statement 1. This is just a confusing mathematical and biochemical statement
in either case.
In the
hierarchy of limitations of Michaelis-Menten equation, its maximum velocity
constitutes the second level of limitations, while its independent variable,
that is the substrate (CO2), constitutes the first level of the limitations.
It is clear
that “Rubisco-limited hypothesis” is incorrect, both mathematically and
biochemically, otherwise the principles of biochemistry and enzyme kinetics
would have been changed by now. What is not clear and difficult to understand
or ignore, is that the model of Farquhar et al rejects the principles of
Michaelis-Menten in its Rubisco-limited theory, but uses Michaelis-Menten
equation in that same model. It is not possible to have it both ways.
06/23/05 23:46:38
Martin wrote:
Hello Hadi,
In your
answer to the first question you consider that in a multi-substrate reaction
only one enzyme-substrate complex can be limiting and that woud be the
rate-determining step. Now, let E be the enzyme-substrate form of the first
step in a two substrate reaction. In a reaction with the second substrate (B),
K1.E.B=(k2+k3)EB; the rate of reaction V=k3.EB is limited by EB or by either E
or B. If the limitation of E is similar to the limitation of Rubisco in
Rubisco-limited hypothesis, what is wrong with it.
07/04/05 15:28:55
hadi wrote:
Hello Martin:
Thank you for
your question. If my interpretation is correct, your E can be similar to fully
activated RuBP saturated Rubisco, and you want to see what is wrong with
limitations of either RuBP saturated Rubisco or CO2.
My answer is
that there is nothing wrong with this, and that is why it has been so
confusing. In fact this is the perception of most users of this model.
Interestingly, the hypothesis of Farquhar et al is slightly different from this.
Let’s look at von Caemmerer & Farquhar (1981). At the end of the abstract
you see:
“…. These
results are consistent with the hypothesis that CO2 assimilation rate is
limited by the RuP2 saturated rate of the RuP2 carboxylase-oxygenase at low
intercellular p(CO2) and by the rate allowed by RuP2 regeneration capacity at
high intercellular p(CO2).”
Now, if you
check closely, you find that the hypothesis considers Rubisco limitation “at
low p(CO2) and…” This is slightly different from your view of limitation of
“either RuBisco or CO2”, but it makes a drastic difference in the outcome of
hypothesis. A limitation of Rubisco at low CO2 does not allow carboxylation to
increase any further, no matter how much you increase p(CO2). In fact Rubisco
would still be the limiting factor “at high intercellular p(CO2), which
invalidates the second part of the hypothesis.
Indeed, the
phrase of “Rubisco limitation at low CO2” is contradictory from within. At low
CO2, Co2 is limiting, and when Rubisco is limiting, the reaction reaches its
saturation level. The condition imposed by this phrase is impossible to meet.
If fully
activated RuBP saturated Rubisco is limited at CO2 compensation point, it means
zero net photosynthesis at any CO2 concentration, zero plant growth, zero
animal growth. This theory cannot be valid.
07/05/05 18:52:41
Cal wrote:
Hi Hadi:
Thank you for
your very inspiring comments. In response to Hugh, I would like to add, if I
may, that the model users have always been seeking help. Look at the following
S.O.S. message. It is public, from the internet.
"The
MEDRUSH Vegetation Model C.P. Osborne and F.I. Woodward Dept. of Animal and
Plant Sciences, University of Sheffield, Sheffield S10 2TN, U.K. August 1999
Please notify
the authors of any errors in this description - contact
c.p.osborne@sheffield.ac.uk
The widely
used model of Farquhar et al. (1980) describes leaf CO2-exchange, where
steady-state photosynthesis is controlled by either the capacity to regenerate
Ribulose-1,5bisphosphate (RubP) or the carboxylation capacity of RubP
carboxylase / oxygenase"
Thanks again.
Cal
07/07/05 07:18:45
hadi wrote:
Hi Cal,
Rubisco
reacts with both RuBP and CO2; with RuBP binding first and CO2 next. Thus, if
it is a limitation of either Rubisco or RuBP regeneration, it comes back to the
limitation of RuBP saturated Rubisco at low CO2 levels and RuBP at high CO2
levels. It does not make any difference.
What I can
say is that Rubisco can never be limiting at low CO2, i.e. Both parts of the
theory of Farquhar et al are invalid.
07/07/05 11:22:11
Brad wrote:
Hello Hadi:
I have seen
another interpretation of the model of Farquhar et al, that is:
The steep
part of the response of assimilation rate to p(CO2) follows the RuBP saturated
kinetics of Rubisco, but the flat part is RuBP limited.
What is your
opinion?
Thanks
07/17/05 12:33:44