
Citation: Jehad Shaikhali, Gunnar Wingsle. Redox-regulated transcription in plants: Emerging concepts[J]. AIMS Molecular Science, 2017, 4(3): 301-338. doi: 10.3934/molsci.2017.3.301
[1] | Maya Briani, Benedetto Piccoli . Fluvial to torrential phase transition in open canals. Networks and Heterogeneous Media, 2018, 13(4): 663-690. doi: 10.3934/nhm.2018030 |
[2] | Xavier Litrico, Vincent Fromion . Modal decomposition of linearized open channel flow. Networks and Heterogeneous Media, 2009, 4(2): 325-357. doi: 10.3934/nhm.2009.4.325 |
[3] | Graziano Guerra, Michael Herty, Francesca Marcellini . Modeling and analysis of pooled stepped chutes. Networks and Heterogeneous Media, 2011, 6(4): 665-679. doi: 10.3934/nhm.2011.6.665 |
[4] | Didier Georges . Infinite-dimensional nonlinear predictive control design for open-channel hydraulic systems. Networks and Heterogeneous Media, 2009, 4(2): 267-285. doi: 10.3934/nhm.2009.4.267 |
[5] | Rudy R. Negenborn, Peter-Jules van Overloop, Tamás Keviczky, Bart De Schutter . Distributed model predictive control of irrigation canals. Networks and Heterogeneous Media, 2009, 4(2): 359-380. doi: 10.3934/nhm.2009.4.359 |
[6] | Nora Aïssiouene, Marie-Odile Bristeau, Edwige Godlewski, Jacques Sainte-Marie . A combined finite volume - finite element scheme for a dispersive shallow water system. Networks and Heterogeneous Media, 2016, 11(1): 1-27. doi: 10.3934/nhm.2016.11.1 |
[7] | Jacek Banasiak, Proscovia Namayanja . Asymptotic behaviour of flows on reducible networks. Networks and Heterogeneous Media, 2014, 9(2): 197-216. doi: 10.3934/nhm.2014.9.197 |
[8] | Avner Friedman . PDE problems arising in mathematical biology. Networks and Heterogeneous Media, 2012, 7(4): 691-703. doi: 10.3934/nhm.2012.7.691 |
[9] | Ye Sun, Daniel B. Work . Error bounds for Kalman filters on traffic networks. Networks and Heterogeneous Media, 2018, 13(2): 261-295. doi: 10.3934/nhm.2018012 |
[10] | Gildas Besançon, Didier Georges, Zohra Benayache . Towards nonlinear delay-based control for convection-like distributed systems: The example of water flow control in open channel systems. Networks and Heterogeneous Media, 2009, 4(2): 211-221. doi: 10.3934/nhm.2009.4.211 |
The dynamics of network flows is usually modelled by systems of Partial Differential Equations (briefly PDEs), most of time balance laws. The dynamics is defined on a topological graph with evolution on arcs given by system of PDEs, while additional conditions must be assigned at network nodes, e.g. conservation of mass and momentum. There is a large literature devoted to these problems and we refer to [5] for a extensive survey and for additional references.
In particular, here we focus on water flows on a oriented network of open canals and the model given by Saint-Venant or shallow water equations. The latter form a non linear system of balance laws composed by a mass and momentum balance laws. In water management problems, these equations are often used as a fundamental tool to describe the dynamics of canals and rivers, see [1] and papers in same volume, and various control techniques were proposed, see [2,3,17,15,19,23,26] and references therein. Moreover, the need of dynamic models in water management is well documented, see [25]. The shallow water system is hyperbolic (except when water mass vanishes) and has two genuinely nonlinear characteristic fields. Moreover, it exhibits two regimes: fluvial or sub-critical, when one eigenvalue is negative and one positive, and torrential or super-critical, when both eigenvalues are positive. This is captured by the so called Froude number, see (1). For a complete description of the physics of the problem one needs to supply the equations with conditions at nodes, which represent junctions. The junction conditions are originally derived by engineers in the modeling of the dynamic of canals and rivers. The first and most natural condition is the conservation of water mass which is expressed as the equality between the sum of fluxes from the incoming canals and that from outgoing ones. One single condition is not sufficient to isolate a unique solution, thus different additional condition were proposed in the literature. Physical reasons motivate different choices of conditions, among which the equality of water levels, of energy levels and conservation of energy. For the assessment of coupling conditions on canals networks and for more details on the existence of solutions in the case of subcritical flows, we refer the reader to [9,18,16,20,14,22,24]. For discussion on supercritical flow regimes, we refer the reader to [18] and references there in.
Then, to construct solutions one may resort to the concept of Riemann solver at a junction, see [13]. A Riemann solver at a junction is a map assigning solutions to initial data which are constant on each arc. Alternatively one may assign boundary conditions on each arc, but, due to the nonlinearity of equations, one has to make sure that boundary values are attained. This amounts to look for solutions with waves having negative speed on incoming channels and positive on outgoing ones: in other words waves do not enter the junction. A Riemann solver with such characteristics is called consistent, see also [12].
In this paper we are interested in transitions between different flow regimes, when the transition occurs at a junction of a canals network. We assume to have incoming canals which end at the junction and outgoing canals which start at the junction. Thus we formulate a left-half Riemann problem for incoming canals and a right-half Riemann problem for outgoing canals to define the region of admissible states such that waves do not propagate into the junction. This corresponds to identify the regions where Riemann solvers can take values in order to be consistent. Such regions are enclosed by the Lax curves (and inverted Lax curves) and the regime change curves. To help the geometric intuition, we developed pictures showing such curves and the regions they enclose.
The definitions described above and given in Section 4, are the necessary basis for an analysis on a complex network. Due to the complexity of the problem, we consider as case study the specific case of two identical canals interconnected at a junction (simple junction). We start focusing on conservation of water through the junction and equal height as coupling conditions. It is typically expected the downstream flow to be more regular, thus we consider three cases: fluvial to fluvial, torrential to fluvial and torrential to torrential. In the fluvial to fluvial case there exists a unique solution. However such solution may be different than the solution to the same Riemann problem inside a canal (without the junction) and may exhibit the appearance of a torrential regime. The torrential to fluvial case is more delicate to examine. Three different cases may happen: the solution propagates the fluvial regime upstream, the solution propagates the torrential regime downstream or no solution exits. Finally, in the torrential to torrential case, if the solution exists then it is torrential.
To illustrate the achieved results we perform simulations using a Runge-Kutta Discontinuous Galerkin scheme [6]. The RKDG method is an efficient, effective and compact numerical approach for simulations of water flow in open canals. Specifically, it is a high-order scheme and compact in the sense that the solution on one computational cell depends only on direct neighboring cells via numerical fluxes, thus allowing for easy handling the numerical boundary condition at junctions. In the first example we show a simulation where an upstream torrential regime is formed starting from special fluvial to fluvial conditions. The second example shows how a torrential regime may propagate downstream.
We conclude by discussing the possible solutions if the water height condition is replaced by the equal energy condition.
The paper is organized as follows: in Section 2, we present the model starting from the one-dimensional shallow water equations. In Section 3, we give useful notations and preliminary results that allow to determine the admissible states for the half-Riemann problems discussed in the following Section 4. In Section 5 we study possible solutions at a simple junction for different flow regimes and different junction conditions. Finally, in Section 6 we illustrate the results of the previous section with a couple of numerical tests.
The most common and interesting method of classifying open-channel flows is by dimensionless Froude number, which for a rectangular or very wide channel is given by the formula:
Fr=|v|√gh, | (1) |
where
●
●
●
The Froude-number denominator
We are interested in the transition between different flow regimes when it occurs at a junction of a canals network. On each canal the dynamics of water flow is described by the following system of one-dimensional shallow water equations
(hhv)t+(hvhv2+12gh2)x=0. | (2) |
The quantity
∂tu+∂xf(u)=0, | (3) |
where
u=(hhv),f(u)=(hvhv2+12gh2). | (4) |
For smooth solutions, these equations can be rewritten in quasi-linear form
∂tu+f′(u)∂xu=0, | (5) |
where the Jacobian matrix
f′(u)=(01−v2+gh2v). | (6) |
The eigenvalues of
λ1=v−√gh,λ2=v+√gh, | (7) |
with corresponding eigenvectors
r1=(1λ1),r2=(1λ2). | (8) |
The shallow water equations are strictly hyperbolic away from
Solutions to systems of conservation laws are usually constructed via Glimm scheme of wave-front tracking [10,21]. The latter is based on the solution to Rieman problems:
{∂tu+∂xf(u)=0,u(x,0)={ul if x<0,ur if x>0. | (9) |
Here
(R) Centered Rarefaction Waves. Assume
u(x,t)={u− for x<λi(u−)t,Ri(x/t;u−) for λi(u−)t≤x≤λi(u+)t,u+ for x>λi(u+)t, |
where, for the 1-family
R1(ξ;u−):=(19(v−+2√h−−ξ)2127(v−+2√h−+2ξ)(v−+2√h−−ξ)2) |
for
R2(ξ;u−):=(19(−v−+2√h−−ξ)2127(v−2√h−+2ξ)(−v−+2√h−−ξ)2) |
for
(S) Shocks. Assume that the state
u(x,t)={u− if x<λtu+ if x>λt |
provides a piecewise constant solution to the Riemann problem. For strictly hyperbolic systems, where the eigenvalues are distinct, we have that
λi(u+)<λi(u−,u+)<λi(u−),λi(u−,u+)=q+−q−h+−h−. |
To determine a solution for problems on a network, we need to analyze in detail the shape of shocks and rarefaction curves and, more generally, of Lax curves (which are formed by joining shocks and rarefaction ones, see [4]). We start fixing notations and illustrating the shapes of curves.
For a given point
for h<h0,v=R1(h0,v0;h)=v0−2(√gh−√gh0);for h>h0,v=S1(h0,v0;h)=v0−(h−h0)√gh+h02hh0;for h>h0,v=R2(h0,v0;h)=v0−2(√gh0−√gh);for h<h0,v=S2(h0,v0;h)=v0−(h0−h)√gh+h02hh0. | (10) |
Moreover, we define the inverse curves:
for h>h0,v=R−11(h0,v0;h)=v0+2(√gh0−√gh);for h<h0,v=S−11(h0,v0;h)=v0+(h0−h)√gh+h02hh0. | (11) |
Similarly, we set:
for h<h0,v=R−12(h0,v0;h)=v0+2(√gh−√gh0);for h>h0,v=S−12(h0,v0;h)=v0+(h−h0)√gh+h02hh0. | (12) |
We will also consider the regime transition curves: the 1-critical curve is given by
v=C+(h)=√gh | (13) |
and the 2-critical curve by
v=C−(h)=−√gh. | (14) |
In Figure 1 we illustrate the shape of these curves.
To construct a solution to a Riemann problem
ϕl(h):=R1(hl,vl;h)∪S1(hl,vl;h). | (15) |
For the right state
ϕr(h):=R−12(hr,vr;h)∪S−12(hr,vr;h). | (16) |
Remark 1. The Riemann problem for shallow water equations 2 with left state
vl+2√ghl≥vr−2√ghr. | (17) |
When working with
˜ϕl(h)=hϕl(h),˜ϕr(h)=hϕr(h)and˜C+(h)=hC+(h),˜C−(h)=hC−(h). |
Moreover, for a given value
Fi=vi√ghi,or˜Fi=qihi√ghi. | (18) |
In this subsection we study in detail the properties of the function
˜ϕl(h)={h(vl+2√ghl−2√gh),0<h≤hl,h(vl−√g2hl(h−hl)√h+hlh),h>hl |
with
limh→0+˜ϕl(h)=0andlimh→+∞˜ϕl(h)=−∞. |
By computing its first and second derivatives,
˜ϕ′l(h)={vl+2√ghl−3√gh,0<h≤hl,vl−√g2hl(4h2+hlh−h2l2√h(h+hl)),h>hl |
and
˜ϕ′′l(h)={−32√gh,0<h≤hl,−√g2hl(8h3+12hlh+3h2lh+h3l4h(h+hl)√h(h+hl)),h>hl, |
we can conclude that
˜ϕ′l(0)=vl+2√ghl and limh→+∞˜ϕl(h)=−∞ |
we investigate two different cases:
Case 1. If
Case 2. If
Case 2.1. For
h+l,R=19g(vl+2√ghl)2, | (19) |
and we have that the maximum point
˜ϕl(h)=0⇔h=14g(vl+2√ghl)2. |
Notice that for
h−l,R=1g(vl+2√ghl)2; | (20) |
while for
vl−(h−l,S−hl)√gh−l,S+hl2hlh−l,S+√gh−l,S=0; | (21) |
Case 2.2. For
h+l,Ssuch thatvl−(h+l,S−hl)√gh+l,S+hl2hlh+l,S−√gh+l,S=0; | (22) |
and the curve
Notice that for
ql=˜ϕl(h)=hS1(hl,vl;h) |
has two solutions:
h=hlandh=h∗l=hl2(−1+√1+8F2l). | (23) |
Moreover, for
(q2lg)13<hl2(−1+√1+8F2l),forFl>1. |
Indeed, using the relation
Here we study the properties of the function
˜ϕr(h)={h(vr−2√ghr+2√gh),0<h≤hr,h(vr+√g2hr(h−hr)√h+hrh),h>hr. |
By straightforward computations we get its derivatives:
˜ϕ′r(h)={vr−2√ghr+3√gh,0<h≤hr,vr+√g2hr(4h2+hrh−h2r2√h(h+hr)),h>hr. |
˜ϕ′′r(h)={32√gh,0<h≤hr,√g2hr(8h3+12hrh+3h2rh+h3r4h(h+hr)√h(h+hr)),h>hr. |
Then,
˜ϕ′r(0)=vr−2√ghr and limh→+∞˜ϕr(h)=+∞ |
we investigate two different cases:
Case 1. If
Case 2. If
Case 2.1. For
h−r,R=19g(−vr+2√ghr)2 | (24) |
and we have that the minimum point
˜ϕr(h)=0⇔h=14g(−vr+2√ghr)2. |
For
h+r,R=1g(−vr+2√ghr)2, | (25) |
while for
vr+(h+r,S−hr)√gh+r,S+hr2hrh+r,S+√gh+r,S=0. | (26) |
Case 2.2. For
h−r,S such that vr+(hr−h+r,S)√gh−r,S+hr2hrh−r,S+√gh−r,S=0 |
and curve
Notice that the equation
qr=˜ϕr(h)=hS−12(hr,vr;h),h≥hr, |
has two solutions:
h=hrandh=h∗r=hr2(−1+√1+8F2r). | (27) |
Moreover, for
[The case of an incoming canal] We fix a left state and we look for the right states attainable by waves of non-positive speed.
Fix
{∂tu+∂xf(u)=0,u(x,0)={ul if x<0ˆu if x>0 | (28) |
contains only waves with non-positive speed. We distinguish three cases:
● Case A: the left state
● Case B: the left state
● Case C: the left state
For this case we refer to Figure 4.We identify the set
IA1={(ˆh,ˆq):h+l,R≤ˆh≤h−l,S,ˆq=˜ϕl(ˆh)}, | (29) |
where the points
IA2={(ˆh,ˆq):0<ˆh≤h−l,S, ˆq≤ˆhS2(h−l,S,C−(h−l,S);ˆh)}⋃{(ˆh,ˆq):ˆh>h−l,S, ˆq≤˜C−(ˆh)}. | (30) |
The last region
λ(um,ˆu)=qm−ˆqhm−ˆh≤0. |
To define this region, we have to look for values
qm−q=(hm−h)(vm+√g2hm√h(h+hm))≤0,h<hm. |
This inequality is verified for
h∗m=hm2(−1+√1+8F2m). |
We obtain (see Figure 4),
IA3={(ˆh,ˆq): for all (hm,qm) which vary on ˜ϕl such that −1≤˜Fm<0, 0<ˆh≤h∗m, ˆq=ˆhS2(hm,vm;ˆh)}. | (31) |
For this case we refer to Figure 5. It is always possible to connect the left value
h∗l=12(−1+√1+8F2l)hl |
as previously computed in 23. Moreover, as previously observed at the end of subsection 3.0.1 the value
NB(ul)=NA(ul)∖{ˆu=(ˆh,ˆq):h+l,S≤ˆh≤h∗l, ˆq=˜ϕl(ˆh)}, | (32) |
where
For this case we refer to Figure 6. We have that: if
NC(ul)={(ˆh,ˆq):ˆh>0, ˆq<˜C−(ˆh)}; |
otherwise if
NC(ul)={(ˆh,ˆq):0<ˆh≤h−l,R, q<ˆhS2(h−l,R,v−l,R;ˆh)}⋃{(ˆh,ˆq):ˆh>h−l,R, ˆq<˜C−(ˆh)}. | (33) |
[The case of an outgoing canal] We fix a right state and we look for the left states attainable by waves of non-negative speed. For sake of space the figures illustrating these cases will be postponed to the Appendix.
Fix
{∂tu+∂xf(u)=0,u(x,0)={˜u if x<0ur if x>0 | (34) |
contains only waves with non-negative speed. As in the previous case we identify three cases:
● Case A: the right value
● Case B: the right value
● Case C: the right value
For this case we refer to Figure 12 in the Appendix. We identify the set
OA1={(˜h,˜q):h−r,R≤˜h≤h+r,S, ˜q=˜ϕr(˜h)}, | (35) |
where the points
The second region is such that
OA2={(˜h,˜q):0<˜h≤h+r,S, ˜q≥˜hS−11(h+r,S,v+r,S;˜h)}⋃{˜h≥h+r,S, ˜q≥˜C+(˜h)}. | (36) |
The third region is defined by the set of all possible left states
λ(um,˜u)=qm−˜qhm−˜h≥0. |
To define this region we have to look for values
OA3={(˜h,˜q): for all (hm,qm) which vary on ˜ϕr such that 0<˜Fm≤1 0<˜h≤h∗m, ˜q=˜hS−11(hm,vm;˜h)}. | (37) |
For this case we refer to Figure 13 in the Appendix. If
PB(ur)={(˜h,˜q): ˜h≥0, ˜q≥˜C+(˜h)}; |
otherwise, if
PB(ur)={(˜h,˜q): 0<˜h≤h+r,R, ˜q≥˜hS−11(u−r,R;˜h)}⋃{(˜h,˜q),˜h>h−r,R, ˜q≥˜C+(˜h)}. | (38) |
For this case we refer to Figure 14 in the Appendix. It is always possible to connect the right value
h∗r=12(−1+√1+8F2r)hr |
as done in 27. Moreover, as previously observed at the end of subsection 3.0.2, the point
PC(ur)=PA(u∗r)∖{(h,q):h−r,S≤h≤h∗r, q=˜ϕr(h)}, | (39) |
where
We consider here as case study a fictitious network formed by two canals intersecting at one single point, which artificially represents the junction. The junction is straight and separates two equal canals, one is the continuation of the other. This simple scenario appears to be like considering a problem for one straight canal, but by adding a fictitious junction we mimic a network and we provide the first analysis necessary for addressing more complicated networks for which the solution strongly depends on the given assumptions at the junction.
We name the canals such that 1 is the incoming canal and 2 is the outgoing ones. We indicate by
A Riemann Problem at a junction is a Cauchy Problem with initial data which are constant on each canal incident at the junction. So, assuming constant initial conditions
qb1=qb2 | (40) |
and equal heights
hb1=hb2. | (41) |
In the following we study the boundary solution
Case A
{ub1∈NA(ul),ub2∈PA(ur),qb1=qb2=qb,hb1=hb2, | (42) |
with
Proposition 1. Under the subcritical condition on
Proof. We distinguish two cases:
Case 1. The two curves
Case 2. The two curves
ub1=ub2=u+l,R. | (43) |
If
ub1=ub2=u−r,R. | (44) |
Remark 2. Notice that the proposed procedure may give a solution which is different from the classical solution of the Riemann problem on a single channel, given by the intersection point of
Case B
{ub1∈NB(ul),ub2∈PA(ur),qb1=qb2=qb,hb1=hb2, | (45) |
with
Proposition 2. System 45 admits a solution if the two regions
Proof. We distinguish two cases:
Case 1. The two curves
Case 2. The two curves
Case 2.1. Referring to Figure 16, the point
Case 2.2. Referring Figure 17, if
Case B
Assuming different conditions at the junction give rise to new possible solutions. In canals network problems, it is usual to couple the conservation of the mass with the conservation of energy at the junctions. The specific energy
E=h+v22g. | (46) |
For a given flow rate, there are usually two states possible for the same specific energy. Studying
h=hc=(q2g)13. | (47) |
Critical depth
In our case, assuming equal energy at the junction gives
v212+gh1=v222+gh2. | (48) |
Moreover, assuming
gh1F212+gh1=gh31F212h22+gh2, |
where
v21=gh1F21 and v22=v21h21h22=gh31F21h22. |
Then, we have two possible solution for the heights values at the junction:
hb1=hb2 (equal heigths) | (49) |
or
hb2hb1=F214(1+√1+8F21). | (50) |
So, for
Remark 3. In the case of a simple junction, the natural assumption (consistent with the dynamic of shallow-water equations) should be to assume the conservation of the momentum. With our notation, the relation 49 or 48 sholud be replaced by the following:
q21h1+12gh21=q22h2+12gh21. | (51) |
By the same reasoning used before in the case of the conservation of energy, from 51 we get
(h2h1)3−(2F21+1)(h2h1)+2F21=0. |
Then, we have again two possible relations for the heights values at the junction:
hb1=hb2 (equal heigths) | (52) |
or
hb2hb1=12(−1+√1+8F21). | (53) |
So again, for
Let us conclude observing that for appropriate values of
In this Section we illustrate the results of Section 5 by means of numerical simulations. We first give a sketch of the adopted numerical procedure and then we focus on two numerical tests which illustrate the regime transitions from fluvial to torrential and viceversa. The latter depend on well chosen initial conditions for Riemann problems at the junction.
We consider again a network formed by two canals intersecting at one single point, which represents the junction. Following [6], we use a high order Runge-Kutta Discontinuous Galerkin scheme to numerically solve system 3 on both canals 1 and 2:
∂tu1+∂xf(u1)=0,for x<0,∂tu2+∂xf(u2)=0,for x<0. | (54) |
The 1D domain of each canal is discretized into cells
∫Cmw(x)∂tUdx=∫Cmf(U)∂xw(x)dx−(ˆfm+12w−m+12−ˆfm−12w+m−12). | (55) |
Terms
u1(x,t)=k∑l=0ˆu1,lm(t)ψlm(x), | (56) |
where
Once the numerical procedure on both canals has been settled, the two systems in 55 have to be coupled with boundary conditions. At the junction the boundary values is settled as follows: at each time step and at each RK stage via the method-of-line approach, we set as left state in 42 (or 45) the approximate solution from canal 1 at the left limit of the junction, i.e.
ul≈Ul=limx→x−M+12U1(x,⋅) |
with
ur≈Ur=limx→x+,212U2(x,⋅), |
with
ˆfM+12≐f(ub1)for the canal 1 ,ˆf12≐f(ub2)for the canal 2 . |
Finally, in our simulations we assume Neumann boundary conditions at the free extremity of the channels.
Applying this numerical procedure, in Figure 10 and 11 we give two examples which illustrate the solution that is obtained in the regime transitions from fluvial to torrential and viceversa. In Figure 10, we assume to have a starting configuration given by the following subcritical constant states:
This paper deals with open canal networks. The interest stems out of applications such as irrigation channels water management. We base our investigations on the well-known Saint-Venant or shallow water equations. Two regimes exist for this hyperbolic system of balance laws: the fluvial, corresponding to eigenvalues with different sign, and the torrential, corresponding to both positive eigenvalues. Most authors focused the attention on designing and analysing network dynamics for the fluvial regime, while here we extend the theory to include regime transitions. After analyzing the Lax curves for incoming and outgoing canals, we provide admissibility conditions for Riemann solvers, describing solutions for constant initial data on each canal. Such analysis allows to define uniquely dynamics according to a set of conditions at junctions, such as conservation of mass, equal water height or equal energy. More precisely, the simple case of one incoming and outgoing canal is treated showing that, already in this simple example, regimes transitions appear naturally at junctions. Our analysis is then visualized by numerical simulations based on Runge-Kutta Discontinuous Galerkin methods.
M. Briani is a member of the INdAM Research group GNCS.
Here we collect additional figures illustrating attainable regions for half-riemann problems and solutions for a simple channel. Figures 12-14 refer to the right-half Riemann problem described in Section 4.2. They show the regions of admissible states such that waves on the outgoing canals do not propagate into the junction, given a right state
Figures 15-18 refer to Section 5 in which we study the possible solutions at a simple junction for different flow regimes, assuming the conservation of mass and equal heights at the junction. Specifically, Figures 15-17 illustrate the possible configurations and their associated solution that may occur during the transition from torrential to fluvial regime. The last Figure 18 shows instead the only possible configuration that admits a solution for the torrential flow regime.
[1] |
Bryant DA, Frigaard N-U (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14: 488-496. doi: 10.1016/j.tim.2006.09.001
![]() |
[2] | Allen JF, Martin W (2007) Out of thin air. Nature 445: 612-614. |
[3] | Hohmann-Mariott MF, Blankenship RE (2012) The photosynthetic world, In: Eaton-Rye JJ, Trypathy BC, Sharkey TD, et al., Photosynthesis: Plastid Biology, Energy Conversion and Carbon Assimilation, Springer. |
[4] |
Horton P, Ruban AV, Walters RG (1996) Regulation of light harvesting in green plants. Annu Rev Plant Physiol Plant Mol Biol 47: 655-684. doi: 10.1146/annurev.arplant.47.1.655
![]() |
[5] |
Aro EM, McCaffery S, Anderson JM (1993) Photoinhibition and D1 protein degradation in peas acclimated to different growth irradiance. Plant Physiol 103: 835-843. doi: 10.1104/pp.103.3.835
![]() |
[6] | Aro EM, Virgin I, Anderson JM (1993) Photoinhibition of photosystem II: inactivation, protein damage and turnover. Biochem Biophys Acta 1143: 113-134. |
[7] |
Gollan PJ, Tikkanen M, Aro EM (2015) Photosynthetic light reactions: integral to chloroplast retrograde signalling. Curr Opin Plant Biol 27: 180-191. doi: 10.1016/j.pbi.2015.07.006
![]() |
[8] | Hossain MS, Dietz KJ (2016) Tuning of redox regulatory mechanisms, reactive oxygen species and redox homeostasis under salinity stress. Front Plant Sci 7: 548. |
[9] |
Foyer CH, Noctor G (2005) Redox homeostasis and antioxidant signalling: a metabolic interface between stress perception and physiological responses. Plant Cell 17: 1866-1875. doi: 10.1105/tpc.105.033589
![]() |
[10] |
Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55: 373-399. doi: 10.1146/annurev.arplant.55.031903.141701
![]() |
[11] |
Foyer CH, Ruban AV, Noctor G (2017) Viewing oxidative stress through the lens of oxidative signalling rather than damage. Biochemical J 474: 877-883. doi: 10.1042/BCJ20160814
![]() |
[12] | Sheibe R, Dietz KJ (2012) Reduction–oxidation network for flexible adjustment of cellular metabolism in photoautotrophic cells. Plant Cell Envi 155: 1477-1485. |
[13] |
Dietz KJ, Pfannschmidt T (2011) Novel regulators in photosynthetic redox control of plant metabolism and gene expression. Plant Physiol 155: 1477-1485. doi: 10.1104/pp.110.170043
![]() |
[14] |
Dietz KJ, Turkan I, Krieger-Liszkay A (2016) Redox- and reactive oxygen species-dependent signalling in and from the photosynthesizing chloroplast. Plant Physiol 171: 1541-1550. doi: 10.1104/pp.16.00375
![]() |
[15] | Kleine T, Leister D (2013) retrograde signal galore. Front Plant Sci 4: 45. |
[16] |
Nakayama T, Archibald JM (2012) Evolving a photosynthetic organelle. BMC Biol 10: 35. doi: 10.1186/1741-7007-10-35
![]() |
[17] |
Giege P, Sweetlove LJ, Cognat V, et al. (2005) Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis. Plant Cell 17: 1497-1512. doi: 10.1105/tpc.104.030254
![]() |
[18] |
Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9: 383-395. doi: 10.1038/nrg2348
![]() |
[19] |
Bradbeer JW, Atkinson YE, Borner T, et al. (1979) Cytoplasmic synthesis of plastid polypeptides may be controlled by plastid-synthesized RNA. Nature 279: 816-817. doi: 10.1038/279816a0
![]() |
[20] |
Oelmuller R, Levitan I, Bergfeld R, et al. (1986). Expression of nuclear genes as affected by treatments acting on the plastids. Planta 168: 482-492. doi: 10.1007/BF00392267
![]() |
[21] |
Susek RE, Ausubel FM, Chory J (1993) Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell 74: 787-799. doi: 10.1016/0092-8674(93)90459-4
![]() |
[22] |
Yoshida R, Sato T, Kanno A, et al. (1998) Streptomycin mimics the cool temperature response in rice plants. J Exp Bot 49: 221-227. doi: 10.1093/jxb/49.319.221
![]() |
[23] |
Sullivan JA, Gray JC (1999). Plastid translation is required for the expression of nuclear photosynthesis genes in the dark and in roots of the pea lip1 mutant. Plant Cell 11: 901-910. doi: 10.1105/tpc.11.5.901
![]() |
[24] |
Pogson BJ, Woo NS, Förster B, et al. (2008) Plastid signalling to the nucleus and beyond. Trends Plant Sci 13: 602-609. doi: 10.1016/j.tplants.2008.08.008
![]() |
[25] |
Chi W, Feng P, Ma J, et al. (2015) Metabolites and chloroplast retrograde signaling. Curr Opin Plant Biol 25: 32-38. doi: 10.1016/j.pbi.2015.04.006
![]() |
[26] | Chan KX, Phua SY, Crisp P, et al. (2015) Learning the languages of the chloroplast: retrograde signaling and beyond. Annu Rev Plant Biol 67: 25-53. |
[27] | Estavillo GM, Chan KX, Phua SY, et al. (2013) Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast. Front Plant Sci 3: 300. |
[28] |
Xiao Y, Savchenko T, Baidoo EE, et al. (2012) Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes. Cell 149: 1525-1535. doi: 10.1016/j.cell.2012.04.038
![]() |
[29] |
Estavillo GM, Crisp PA, Pornsiriwong W, et al. (2011) Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis. Plant Cell 23: 3992-4012. doi: 10.1105/tpc.111.091033
![]() |
[30] |
Ramel F, Birtic S, Ginies C, et al. (2012) Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants. Proc Natl Acad Sci USA 109: 5535-5540. doi: 10.1073/pnas.1115982109
![]() |
[31] |
Woodson JD, Perez-Ruiz JM, Chory J (2011). Heme synthesis by plastid ferrochelatase I regulates nuclear gene expression in plants. Curr Biol 21: 897-903. doi: 10.1016/j.cub.2011.04.004
![]() |
[32] |
Kropat J, Oster U, Rüdiger W, et al. (1997) Chlorophyll precursors are signals of chloroplast origin involved in light induction of nuclear heat-shock genes. Proc Natl Acad Sci USA 94: 14168-14172. doi: 10.1073/pnas.94.25.14168
![]() |
[33] |
Kropat J, Oster U, Rudiger W, et al. (2000) Chloroplast signaling in the light induction of nuclear HSP70 genes requires the accumulation of chlorophyll precursors and their accessibility to cytoplasm/nucleus. Plant J 24: 523-531. doi: 10.1046/j.1365-313x.2000.00898.x
![]() |
[34] |
Strand A, Asami T, Alonso J, et al. (2003) Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature 421: 79-83. doi: 10.1038/nature01204
![]() |
[35] |
Zhang ZW, Yuan S, Feng H, et al. (2011) Transient accumulation of Mg-protoporphyrinIX regulates expression of PhANGs: new evidence for the signaling role of tetrapyrroles in mature Arabidopsis plants. J Plant Physiol 168: 714-721. doi: 10.1016/j.jplph.2010.10.016
![]() |
[36] |
Susek RE, Ausubel FM, Chory J (1993) Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell 74: 787-799. doi: 10.1016/0092-8674(93)90459-4
![]() |
[37] |
Mochizuki N, Brusslan JA, Larkin R, et al. (2001) Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci USA 98: 2053-2058. doi: 10.1073/pnas.98.4.2053
![]() |
[38] |
Larkin RM, Alonso JM, Ecker JR, et al. (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299: 902-906. doi: 10.1126/science.1079978
![]() |
[39] |
Koussevitzky S, Nott A, Mockler TC, et al. (2007) Signals from chloroplasts converge to regulate nuclear gene expression. Science 316: 715-719. doi: 10.1126/science. 1140516
![]() |
[40] |
Ankele E, Kindgren P, Pesquet E, et al. (2007) In vivo visualization of Mg-protoporphyrinIX, a coordinator of photosynthetic gene expression in the nucleus and the chloroplast. Plant Cell 19: 1964-1979. doi: 10.1105/tpc.106.048744
![]() |
[41] |
Mochizuki N, Tanaka R, Tanaka A, et al. (2008). The steady-state level of Mg-protoporphyrin IX is not a determinant of plastid-to-nucleus signaling in Arabidopsis. Proc Natl Acad Sci USA 105: 15184-15189. doi: 10.1073/pnas.0803245105
![]() |
[42] |
Moulin M, McCormac AC, Terry MJ, et al. (2008). Tetrapyrrole profiling in Arabidopsis seedlings reveals that retrograde plastid nuclear signaling is not due to Mg-protoporphyrin IX accumulation. Proc Natl Acad Sci USA 105: 15178-15183. doi: 10.1073/pnas.0803054105
![]() |
[43] | Kindgren P, Noren L, Barajas Lopez J, et al. (2011) Interplay between HEAT SHOCK PROTEIN 90 and HY5 controls PhANG expression in response to the GUN5 plastid signal. Mol Plant 5: 901-913. |
[44] |
Kindgren P, Eriksson MJ, Benedict C, et al. (2011) A novel proteomic approach reveals a role for Mg-protoporphyrinIX in response to oxidative stress. Physiol Plant 141: 310-320. doi: 10.1111/j.1399-3054.2010.01440.x
![]() |
[45] |
Lee HC, Hon T, Zhang L (2002) The molecular chaperone Hsp90 mediates heme activation of the yeast transcriptional activator Hap1. J Biol Chem 277: 7430-7437. doi: 10.1074/jbc.M106951200
![]() |
[46] |
Cordoba E, Salmi M, Leon P (2009). Unravelling the regulatory mechanisms that modulate the MEP pathway in higher plants. J Exp Bot 60: 2933-2943. doi: 10.1093/jxb/erp190
![]() |
[47] |
Rodríguez-Concepción M (2006) Early steps in isoprenoid biosynthesis: multilevel regulation of the supply of common precursors in plant cells. Phytochem Rev 5: 1-15. doi: 10.1007/s11101-005-3130-4
![]() |
[48] |
Rossel JB, Walter PB, Hendrickson L, et al. (2006) A mutation affecting ASCORBATE PEROXIDASE 2 gene expression reveals a link between responses to high light and drought tolerance. Plant Cell Environ 29: 269-281. doi: 10.1111/j.1365-3040.2005.01419.x
![]() |
[49] |
Wilson PB, Estavillo GM, Field KJ, et al. (2009) The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis. Plant J 58: 299-317. doi: 10.1111/j.1365-313X.2008.03780.x
![]() |
[50] |
Estavillo GM, Crisp PA, Pornsiriwong W, et al. (2011) Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis. Plant Cell 23: 3992-4012. doi: 10.1105/tpc.111.091033
![]() |
[51] |
Gigolashvili T, Geier M, Ashykhmina N, et al. (2012) The Arabidopsis thylakoid ADP/ATP carrier TAAC has an additional role in supplying plastidic phosphoadenosine 5′-phosphosulfate to the cytosol. Plant Cell 24: 4187-4204. doi: 10.1105/tpc.112.101964
![]() |
[52] |
Gy I, Gasciolli V, Lauressergues D, et al. (2007) Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19: 3451-3461. doi: 10.1105/tpc.107.055319
![]() |
[53] |
Kim C, Apel K (2013) Singlet oxygen-mediated signaling in plants: moving from flu to wild type reveals an increasing complexity. Photosynth Res 116: 455-464. doi: 10.1007/s11120-013-9876-4
![]() |
[54] |
Op den Camp RGL, Przybyla D, Ochsenbein C, et al. (2003) Rapid induction of distinct stress responses after the release of singlet oxygen in Arabidopsis. Plant Cell 15: 2320-2332. doi: 10.1105/tpc.014662
![]() |
[55] |
Von Gromoff ED, Alawady A, Meinecke L, et al. (2008) Heme, a plastid-derived regulator of nuclear gene expression in chlamydomonas. Plant Cell 20: 552-567. doi: 10.1105/tpc.107.054650
![]() |
[56] |
Voss B, Meinecke L, Kurz T, et al. (2011) Hemin and magnesium-protoporphyrinIX induce global changes in gene expression in Chlamydomonas reinhardtii. Plant Physiol 155: 892-905. doi: 10.1104/pp.110.158683
![]() |
[57] |
Espinas NA, Kobayashi K, Takahashi S, et al. (2012). Evaluation of unbound free heme in plant cells by differential acetone extraction. Plant Cell Physiol 53: 1344-1354. doi: 10.1093/pcp/pcs067
![]() |
[58] |
Zhang L, Hach A (1999) Molecular mechanism of heme signaling in yeast: the transcriptional activator Hap1 serves as the key mediator. Cell Mo Life Sci. 56: 415-426. doi: 10.1007/s000180050442
![]() |
[59] |
Baier M, Dietz K-J (2005) Chloroplasts as source and target of cellular redox regulation: a discussion on chloroplast redox signals in the context of plant physiology. J Exp Bot 56: 1449-1462. doi: 10.1093/jxb/eri161
![]() |
[60] | Gollan PJ, Tikkanen M, Aro EM (2017) Photosynthetic light reactions: integral to chloroplast retrograde signalling. Curr Opin Plant Biol 27: 180-191. |
[61] | Barajas-Lopez JD, Blanco NE, Strand A(2013) Plastid-to-nucleus communication, signals controlling the running of the plant cell. Biochem Biophys Acta 1833: 425-437. |
[62] | Pfalz J, Liebers M, Hirth M, et al. (2012) Environmental control of plant nuclear gene expression by chloroplast redox signals. Front Plant Sci 3: 257. |
[63] |
Jung HS, Mockler TC (2014) A new alternative in plant retrograde signaling. Genome Biol 15: 117. doi: 10.1186/gb4178
![]() |
[64] |
Escoubas J-M, Lomas M, LaRoche S, et al. (1995) Light intensity regulation of cab gene transcription is signalled by the redox state of the plastoquinone pool. Proc Natl Acad Sci USA 92: 10237-10241. doi: 10.1073/pnas.92.22.10237
![]() |
[65] |
Maxwell DP, Laudenbach DE, Huner NPA (1995) Redox regulation of light-harvesting complex II and cab mRNA abundance in Dunaliella salina. Plant Physiol 109: 787-795. doi: 10.1104/pp.109.3.787
![]() |
[66] |
Maxwell DP, Falk S, Trick GC, et al. (1994) Growth at low temperature mimics high-light acclimation in Chlorella vulgaris. Plant Physiol 105: 535-543. doi: 10.1104/pp.105.2.535
![]() |
[67] |
Maxwell DP, Laudenbach DE, Huner N (1995) Redox regulation of light-harvesting complex II and cab mRNA abundance in Dunaliella salina. Plant Physiol 109: 787-795. doi: 10.1104/pp.109.3.787
![]() |
[68] | Pfannschmidt T, Nilsson A, Tullberg A, et al. (1999) Direct transcriptional control of the chloroplast genes psbA and psaAB adjusts photosynthesis to light energy distribution in plants IUBMB Life 48: 271-276. |
[69] |
Pfannschmidt T, Schütze K, Brost M, et al. (2001) A novel mechanism of nuclear photosynthesis gene regulation by redox signals from the chloroplast during photosystem stoichiometry adjustment. J Biol Chem 276: 36125-36130. doi: 10.1074/jbc.M105701200
![]() |
[70] |
Oswald O, Martin T, Dominy PJ, et al. (2001) Plastid redox state and sugars: interactive regulators of nuclear-encoded photosynthetic gene expression. Proc Natl Acad Sci USA 98: 2047-2052. doi: 10.1073/pnas.98.4.2047
![]() |
[71] | Hihara Y, Sonoike K, Kanehisa M, et al. (2003) DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 185: 1719-1725. |
[72] |
Fey V, Wagner R, Brautigam K, et al. (2005) Retrograde plastid redox signals in the expression of nuclear genes for chloroplast proteins of Arabidopsis thaliana. J Biol Chem 280: 5318-5328. doi: 10.1074/jbc.M406358200
![]() |
[73] |
Piippo M, Allahverdiyeva Y, Paakkarinen V, et al. (2006) Chloroplast-mediated regulation of nuclear genes in Arabidopsis thalianain the absence of light stress. Physiol Genomics 25: 142-152. doi: 10.1152/physiolgenomics.00256.2005
![]() |
[74] |
Bräutigam K, Dietzel L, Kleine T, et al. (2009). Dynamic plastid redox signals integrate gene expression and metabolism to induce distinct metabolic states in photosynthetic acclimation in Arabidopsis. Plant Cell 21: 2715-2732. doi: 10.1105/tpc.108.062018
![]() |
[75] |
Shao N, Vallon O, Dent R, et al. (2006) Defects in the cytochrome b6/f complex prevent light-induced expression of nuclear genes involved in chlorophyll biosynthesis. Plant Physiol 141: 1128-1137. doi: 10.1104/pp.106.081059
![]() |
[76] |
Bellaflore S, Barneche F, Peltier G, et al. (2005) State transitions and light adaptation require chloroplast thylakoid protein kinase STN7. Nature 433: 892-895. doi: 10.1038/nature03286
![]() |
[77] | Tikkanen M, Gollan PJ, Mekala NR, et al. (2014) Light-harvesting mutants show differential gene expression upon shift to high light as a consequence of photosynthetic redox and reactive oxygen species metabolism. Philos Trans R Soc London Ser B: Biol Sci 369. |
[78] | Gläßer C, Haberer G, Finkemeierm I, et al. (2014) Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks. Mol Plan 20: 1167-1190 |
[79] |
Jacquot JP, Eklund H, Rouhier N, et al. (2009) Structural and evolutionary aspects of thioredoxin reductases in photosynthetic organisms. Trends Plant Sci 14: 336-343. doi: 10.1016/j.tplants.2009.03.005
![]() |
[80] |
Schürmann P, Buchanan BB (2008) The ferredoxin/thioredoxin system of oxygenic photosynthesis. Antioxid Redox Signal 10: 1235-1274. doi: 10.1089/ars.2007.1931
![]() |
[81] | Serrato AJ, Fernández-Trijueque J, Barajas-López JD, et al. (2013) Plastid thioredoxins: A "one-for-all" redox-signaling system in plants. Front Plant Sci 4: 463. |
[82] |
Meyer Y, Siala W, Bashandy T, et al. (2008) Glutaredoxins and thioredoxins in plants. Biochem Biophys Acta 1783: 589-600. doi: 10.1016/j.bbamcr.2007.10.017
![]() |
[83] |
Romano PGN, Horton P, Gray JE (2004) The Arabidopsis cyclophilins gene family. Plant Physiol 134: 1268-1282. doi: 10.1104/pp.103.022160
![]() |
[84] | Kumari S, Roy S, Singh P, et al. (2013) Cyclophilins: Proteins in search of function. Plant Signal Behav 8. |
[85] |
Chueca A, Sahrawy M, Pagano EA, et al. (2002) Chloroplast fructose-1,6-bisphosphatase: structure and function. Photosynth Res 74: 235-249. doi: 10.1023/A:1021243110495
![]() |
[86] |
Thormählen I, Zupok A, Rescher J, et al. (2017) Thioredoxins Play a Crucial Role in Dynamic Acclimation of Photosynthesis in Fluctuating Light. Mol Plant 10: 168-182. doi: 10.1016/j.molp.2016.11.012
![]() |
[87] |
Dietz KJ (2011) Peroxiredoxins in plants and cyanobacteria. Antioxid Redox Signal 15: 1129-1159. doi: 10.1089/ars.2010.3657
![]() |
[88] |
Tripathi BN, Bhatt I, Dietz KJ (2009) Peroxiredoxins: a less studied component of hydrogen peroxide detoxification in photosynthetic organisms. Protoplasma 235: 3-15. doi: 10.1007/s00709-009-0032-0
![]() |
[89] | Cerveau D, Ouahrani D, Marok MA (2015) Physiological relevance of plant 2-Cys peroxiredoxin overoxidation level and oligomerization status. Plant Cell Environ 39: 103-119. |
[90] |
Serrato AJ, Perez-Ruiz JM, Spinola MC, et al. (2004) A novel NADPH thioredoxin reductase, localized in the chloroplast, which deficiency causes hypersensitivity to abiotic stress in Arabidopsis thaliana. J Biol Chem 279: 43821-43827. doi: 10.1074/jbc.M404696200
![]() |
[91] |
Lepisto A, Pakula E, Toivola J, et al. (2013) Deletion of chloroplast NADPH-dependent thioredoxin reductase results in inability to regulate starch synthesis and causes stunted growth under short-day photoperiods. J Exp Bot 64: 3843-3854. doi: 10.1093/jxb/ert216
![]() |
[92] |
Perez-Ruiz JM, Spinola MC, Kirchsteiger K, et al. (2006) Rice NTRC is a high-efficiency redox system for chloroplast protection against oxidative damage. Plant Cell 18: 2356-2368. doi: 10.1105/tpc.106.041541
![]() |
[93] |
Perez-Ruiz JM, Guinea M, Puerto-Galan L, et al. (2014) NADPH thioredoxin reductase C is involved in redox regulation of the Mg-chelatase I subunit in Arabidopsis thaliana chloroplasts. Mol Plant 7: 1252-1255. doi: 10.1093/mp/ssu032
![]() |
[94] | Thormählen I, Meitzel T, Groysman J, et al. (2015) Thioredoxin f1 and NADPH-dependent thioredoxin reductase C have overlapping functions in regulating photosynthetic metabolism and plant growth in response to varying light conditions. Plant Physiol 169: 1766-1786. |
[95] |
Nikkanen L, Toivola J, Rintamäki E (2016) Crosstalk between chloroplast thioredoxin systems in regulation of photosynthesis. Plant Cell Environ 39: 1691-1705. doi: 10.1111/pce.12718
![]() |
[96] |
Yoshida K, Hisabori T (2016) Two distinct redox cascades cooperatively regulate chloroplast functions and sustain plant viability. Proc Natl Acad Sci 113: E3967-3976. doi: 10.1073/pnas.1604101113
![]() |
[97] |
Baier M, Stroher E, Dietz KJ (2004) The acceptor availability at photosystem I and ABA control nuclear expression of 2-Cys peroxiredoxin-A in Arabidopsis thaliana. Plant Cell Physiol 45: 997-1006. doi: 10.1093/pcp/pch114
![]() |
[98] |
Baier M, Stroher E, Dietz K-J (2004) The acceptor availability at photosystem I and ABA control nuclear expression of 2-Cys peroxiredoxin-A in Arabidopsis thaliana. Plant Cell Physiol 45: 997-1006. doi: 10.1093/pcp/pch114
![]() |
[99] | Shaikhali J, Heiber I, Seidel T, et al. (2008). The redox-sensitive transcription factor Rap2.4a controls nuclear expression of 2-Cys peroxiredoxin A and other chloroplast antioxidant enzymes. BMC Plant Biol 8: 48. |
[100] |
Shaikhali J, Baier M (2010). Ascorbate regulation of 2-Cys peroxiredoxin-A promoter activity is light-dependent. J Plant Physiol 167: 461-467. doi: 10.1016/j.jplph.2009.10.021
![]() |
[101] | Heiber I, Stroher E, Raatz B, et al. (2007) The redox imbalanced mutants of Arabidopsis differentiate signaling pathways for redox regulation of chloroplast antioxidant enzymes. Plant Physiol 143: 774-1788. |
[102] | Hiltscher H, Rudnik R, Shaikhali J, et al. (2014) The radical induced cell death protein 1 (RCD1) supports transcriptional activation of genes for chloroplast antioxidant enzymes. Front Plant Sci 5: 475. |
[103] | Kimura M, Yamamoto YY, Seki M, et al. (2003) Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray. Photochem Photobiol 77: 226-233. |
[104] |
Rossel JB, Wilson IW, Pogson BJ (2002) Global changes in gene expression in response to high light in Arabidopsis. Plant Physiol 130: 1109-1120. doi: 10.1104/pp.005595
![]() |
[105] |
Vandenabeele S, Van der Kelen K, Dat J, et al. (2003) A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Proc Natl Acad Sci USA 100: 16113-16118. doi: 10.1073/pnas.2136610100
![]() |
[106] |
Laloi C, Stachowiak M, Pers-Kamczyc E, et al. (2007) Cross-talk between singlet oxygen-and hydrogen peroxide-dependent signalling of stress responses in Arabidopsis thaliana. Proc Natl Acad Sci USA 104: 672-677. doi: 10.1073/pnas.0609063103
![]() |
[107] |
Desikan R, Mackerness S, Hancock JT, et al. (2001) Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiol 127: 159-172. doi: 10.1104/pp.127.1.159
![]() |
[108] |
Fahnenstich H, Scarpeci TE, Valle EM, et al. (2008) Generation of hydrogen peroxide in chloroplasts of Arabidopsis overexpressing glycolate oxidase as an inducible system to study oxidative stress. Plant Physiol 148: 719-729. doi: 10.1104/pp.108.126789
![]() |
[109] |
Li Z, Wakao S, Fischer BB, et al. (2009) Sensing and responding to excess light. Annu Rev Plant Biol 60: 239-260. doi: 10.1146/annurev.arplant.58.032806.103844
![]() |
[110] |
Bechtold U, Richard O, Zamboni A, et al. (2008) Impact of chloroplastic- and extracellular-sourced ROS on high light-responsive gene expression in Arabidopsis. J Exp Bot 59: 121-133. doi: 10.1093/jxb/erm289
![]() |
[111] |
Gadjev I, Vanderauwera S, Gechev TS, et al. (2006) Transcriptomic footprints disclose specificity of reactive oxygen species signalling in Arabidopsis. Plant Physiol 141: 436-445. doi: 10.1104/pp.106.078717
![]() |
[112] |
Van Breusegem F, Bailey-Serres J, Mittler R (2008) Unraveling the tapestry of networks involving reactive oxygen species in plants. Plant Physiol 147: 978-984. doi: 10.1104/pp.108.122325
![]() |
[113] |
Li T, Li H, Zhang YX, et al. (2011) Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Res 39: 2821-2833. doi: 10.1093/nar/gkq1047
![]() |
[114] |
Vandenabeele S, Vanderauwera S, Vuylsteke M, et al. (2004) Catalase deficiency drastically affects gene expression induced by high light in Arabidopsis thaliana. Plant J 39: 45-58. doi: 10.1111/j.1365-313X.2004.02105.x
![]() |
[115] | Queval G, Hager J, Gakiere B, et al. (2008) Why are literature data for H2O2 contents so variable? A discussion of potential difficulties in the quantitative assay of leaf extracts. J Exp Bot 59: 135-146. |
[116] |
Bienert GP, Møller AL, Kristiansen KA, et al. (2007) Specific aquaporins facilitate the diffusion of hydrogen peroxide across membranes. J Biol Chem 282: 1183-1192. doi: 10.1074/jbc.M603761200
![]() |
[117] |
Henzler T, Steudle E (2000) Transport and metabolic degradation of hydrogen peroxide in Chara corallina: model calculations and measurements with the pressure probe suggest transport of H2O2 across water channels. J Exp Bot 51: 2053-2066. doi: 10.1093/jexbot/51.353.2053
![]() |
[118] |
Mubarakshina MM, Ivanov BN, Naydov IA, et al. (2010) Production and diffusion of chloroplastic H2O2 and its implication to signalling. J Exp Bot 61: 3577-3587. doi: 10.1093/jxb/erq171
![]() |
[119] | Sierla M, Rahikainen M, Salojärvi J, et al. (2012) Apoplastic and chloroplastic redox signaling networks in plant stress responses. Antioxid Redox Signal 18: 2220-2239 . |
[120] |
Møller IM, Sweetlove LJ (2010) ROS signalling-specificity is required. Trends Plant Sci 15: 370-374. doi: 10.1016/j.tplants.2010.04.008
![]() |
[121] |
Caplan JL, Kumar AS, Park E, et al. (2015) Chloroplast stromules function during innate immunity. Dev Cell 34: 45-57. doi: 10.1016/j.devcel.2015.05.011
![]() |
[122] |
Meskauskiene R, Nater M, Goslings D, et al. (2001) FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA 98: 12826-12831. doi: 10.1073/pnas.221252798
![]() |
[123] |
Wagner D, Przybyla D, Op den Camp R, et al. (2004) The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana. Science 306: 1183-1185. doi: 10.1126/science.1103178
![]() |
[124] |
Lee KP, Kim C, Landgraf F, Apel K (2007) EXECUTER1‐and EXECUTER2‐dependent transfer of stress‐related signals from the plastid to the nucleus of Arabidopsis thaliana. Proc Natl Acad Sci USA 104: 10270-10275. doi: 10.1073/pnas.0702061104
![]() |
[125] |
Coll NS, Danon A, Meurer J, et al. (2009) Characterization of soldat8, a suppressor of singlet oxygen-induced cell death in Arabidopsis seedlings. Plant Cell Physiol 50: 707-718. doi: 10.1093/pcp/pcp036
![]() |
[126] |
Meskauskiene R, Wursch M, Laloi C, et al. (2009) A mutation in the Arabidopsis mTERF-related plastid protein SOLDAT10 activates retrograde signaling and suppresses 1O2-induced cell death. Plant J 60: 399-410. doi: 10.1111/j.1365-313X.2009.03965.x
![]() |
[127] | Gauthier A, Idänheimo N, Brosché M, et al. (2011) Characterization of RLSs in Arabidopsis thaliana Proceedings of the 10th International Conference on Reactive Oxygen and Nitrogen Species in Plants. P5. |
[128] |
Joo JH, Wang S, Chen JG, et al. (2005) Different signaling and cell death roles of heterotrimeric G protein alpha and beta subunits in the Arabidopsis oxidative stress response to ozone. Plant Cell 17: 957-970. doi: 10.1105/tpc.104.029603
![]() |
[129] |
Suharsono U, Fujisawa Y, Kawasaki T, et al. (2002) The heterotrimeric G protein alpha subunit acts upstream of the small GTPase Rac in disease resistance of rice. Proc Natl Acad Sci USA 99: 13307-13312. doi: 10.1073/pnas.192244099
![]() |
[130] |
Torres MA, Morales J, Sánchez-Rodríguez C, et al. (2013) Functional interplay between Arabidopsis NADPH oxidases and heterotrimeric G protein. Mol Plant Microbe Interact 26: 686-694. doi: 10.1094/MPMI-10-12-0236-R
![]() |
[131] | Petrov VD, Van Breusegem F. (2012) Hydrogen peroxide a central hub for information flow in plant cells. AoB Plants 2012: pls014. |
[132] |
Noctor G, Foyer F (2016) Intracellular redox compartmentation and ROS-related communication in regulation and signaling. Plant Physiol 171: 1581-1592. doi: 10.1104/pp.16.00346
![]() |
[133] |
König J, Muthuramalingam M, Dietz KJ (2012) Mechanisms and dynamics in the thiol/disulfide redox regulatory network: transmitters, sensors and targets. Curr Opin Plant Biol 15: 261-268. doi: 10.1016/j.pbi.2011.12.002
![]() |
[134] | Chen YI, Wei PC, Hsu JL, et al. (2016) NPGPx (GPx7): a novel oxidative stress sensor/transmitter with multiple roles in redox homeostasis. Am J Transl Res 8: 1626-1640. |
[135] | Miller G, Schlauch K, Tam R, et al. (2009) The plant NADPH oxidase RBOHD mediates rapid systemic signaling in response to diverse stimuli. Science Signal 2: ra45. |
[136] |
Rizhsky L, Davletova S, Liang H, et al. (2004) The zinc finger protein Zat12 is required for cytosolic ascorbate peroxidase 1 expression during oxidative stress in Arabidopsis. J Biol Chem 279: 11736-11743. doi: 10.1074/jbc.M313350200
![]() |
[137] | Dietz KJ (2013) Redox regulation of transcription factors in plant stress acclimation and development. Antioxid Redox Signal 2: 1356-1372. |
[138] |
Marinho SH, Real C, Cyrne L, et al. (2014) Hydrogen peroxide sensing, signaling and regulation of transcription factors. Redox Biol 2: 535-562. doi: 10.1016/j.redox.2014.02.006
![]() |
[139] |
Christman MF, Storz G, Ames BN (1989) OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. Proc Natl Acad Sci USA 86: 3484-3488. doi: 10.1073/pnas.86.10.3484
![]() |
[140] |
Imlay JA (2008) Cellular defenses against superoxide and hydrogen peroxide. Annu Rev Biochem 77: 755-776. doi: 10.1146/annurev.biochem.77.061606.161055
![]() |
[141] |
Zheng M, Aslund F, Storz G (1998) Activation of the OxyR transcription factor by reversible bond formation. Science 279: 1718-1721. doi: 10.1126/science.279.5357.1718
![]() |
[142] |
Lee C, Lee SM, Mukhopadhyay P, et al. (2004) Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. Nat Struct Mol Biol 11: 1179-1185. doi: 10.1038/nsmb856
![]() |
[143] |
Kim SO, Merchant K, Nudelman R, et al. (2002) OxyR: a molecular code for redox-related signaling. Cell 109: 383-396. doi: 10.1016/S0092-8674(02)00723-7
![]() |
[144] | Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2015) AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819: 86-96. |
[145] |
Vogel MO, Moore M, König K, et al. (2014) Fast retrograde signaling in response to high light involves metabolite export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF transcription factors in Arabidopsis. Plant Cell 26: 1151-1165. doi: 10.1105/tpc.113.121061
![]() |
[146] | Alsharafa K, Vogel MO, Oelze ML, et al. (2014) Kinetics of retrograde signalling initiation in the high light response of Arabidopsis thaliana. Philos Trans R Soc Lond B Biol Sci 369. |
[147] |
Wu J, Weiss B (1992) Two-stage induction of the soxRS (superoxide response) regulon of Escherichia coli. J Bacteriol 174: 3915-3920. doi: 10.1128/jb.174.12.3915-3920.1992
![]() |
[148] |
Gu M, Imlay JA (2011) The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide. Mol Microbiol 79: 1136-1150. doi: 10.1111/j.1365-2958.2010.07520.x
![]() |
[149] | Lin ECC (2009) Metabolism is associated with formation of harmful oxygen species (oygen stress), In: J W Lengeler, G Drews, H G Schlegel, Biology of the Prokaryotes, 1 Ed., John Wiley & Sons, 535-536. |
[150] |
Yamasaki K, Kigawa T, Inoue M, et al. (2005) Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell 17: 944-956. doi: 10.1105/tpc.104.026435
![]() |
[151] |
Yamasaki K, Kigawa T, Inoue M, (2004) A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J Mol Biol 337: 49-63. doi: 10.1016/j.jmb.2004.01.015
![]() |
[152] |
Chen L, Zhang L, Yu D (2010) Wounding-induced WRKY8 is involved in basal defense in arabidopsis. Mol Plant Microbe Interact 23: 558-565. doi: 10.1094/MPMI-23-5-0558
![]() |
[153] | Banerjee A and Roychoudhury A (2015) WRKY proteins: signaling and regulation of expression during abiotic stress responses. Scientific World J 2015: 807560. |
[154] |
Yoo KS, Ok SH, Jeong BC, et al. (2011) Single cystathionine β-synthase domain–containing proteins modulate development by regulating the thioredoxin system in Arabidopsis. Plant Cell 23: 3577-3594. doi: 10.1105/tpc.111.089847
![]() |
[155] | Zinta G, Khan A, Abdelgawad H, et al. (2016) Unveiling the redox control of plant reproductive development during abiotic stress. Front Plant Sci 7: 700. |
[156] |
Moye-Rowley WS (2003) Regulation of the transcriptional response to oxidative stress in fungi: similarities and differences. Eukaryot Cell 2: 381-389. doi: 10.1128/EC.2.3.381-389.2003
![]() |
[157] |
Miller G, Mittler R (2006) Could heat shock transcription factors function as hydrogen peroxide sensors in plants? Ann Bot 98: 279-288. doi: 10.1093/aob/mcl107
![]() |
[158] |
Hübel A, Schöffl F (1994) Arabidopsis heat shock factor: isolation and characterization of the gene and the recombinant protein. Plant Mol Biol 26: 353-362. doi: 10.1007/BF00039545
![]() |
[159] |
Jung HS, Crisp PA, Estavillo GM, et al. (2013) Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proc Natl Acad Sci USA 110: 14474-14479. doi: 10.1073/pnas.1311632110
![]() |
[160] |
Giesguth M, Sahm A, Simon S, et al. (2015) Redox-dependent translocation of the heat shock transcription factor AtHSFA8 from the cytosol to the nucleus in Arabidopsis thaliana. FEBS Lett 589: 718-725. doi: 10.1016/j.febslet.2015.01.039
![]() |
[161] |
Eferl R, Wagner EF (2003) AP-1: a double-edged sword in tumorigenesis. Nat Rev Cancer 3: 859-868. doi: 10.1038/nrc1209
![]() |
[162] |
Karin M, Takahashi T, Kapahi P, et al. (2001) Oxidative stress and gene expression: the AP-1 and NF-kappaB connections. Biofactors 15: 87-89. doi: 10.1002/biof.5520150207
![]() |
[163] | Klatt P, Molina EP, De Lacoba MG, et al. (1999) Redox regulation of c-Jun DNA binding by reversible S-glutathiolation. FASEB J 13: 1481-1490. |
[164] |
Ariel FD, Manavella PA, Dezar CA, et al. (2007) The true story of the HD-Zip family. Trends Plant Sci 12: 419-426. doi: 10.1016/j.tplants.2007.08.003
![]() |
[165] |
Tron AE, Bertoncini CW, Chan RL, et al. (2002) Redox regulation of plant homeodomain transcription factors. J Biol Chem 277: 34800-34807. doi: 10.1074/jbc.M203297200
![]() |
[166] |
Comelli RN, Gonzalez DH (2007) Conserved homeodomain cysteines confer redox sensitivity and influence the DNA binding properties of plant class III HD-Zip proteins. Arch Biochem Biophys 467: 41-47. doi: 10.1016/j.abb.2007.08.003
![]() |
[167] |
Kobayashi M, Yamamoto M (2006) Nrf2-Keap1 regulation of cellular defense mechanisms against electrophiles and reactive oxygen species. Adv Enzyme Regul 46: 113-140. doi: 10.1016/j.advenzreg.2006.01.007
![]() |
[168] |
Huang HC, Nguyen T, Pickett CB (2002) Phosphorylation of Nrf2 at Ser-40 by protein kinase C regulates antioxidant response element-mediated transcription. J Biol Chem 277: 42769-42774. doi: 10.1074/jbc.M206911200
![]() |
[169] |
Li P, Wind JJ, Shi X, et al. (2011). Fructose sensitivity is suppressed in Arabidopsis by the transcription factor ANAC089 lacking the membrane-bound domain. Proc Natl Acad Sci USA 108: 3436-3441. doi: 10.1073/pnas.1018665108
![]() |
[170] | Klein P, Seidel T, Stöcker B, et al. (2012) The membrane-tethered transcription factor ANAC089 serves as redox-dependent suppressor of stromal ascorbate peroxidase gene expression. Front Plant Sci 3: 247. |
[171] |
Yang Z-T, WangMJ, Sun L (2014) The membrane-associated transcription factor NAC089 controls ER-stress-induced programmed cell death in plants. PLoS Genet 10: e1004243. doi: 10.1371/journal.pgen.1004243
![]() |
[172] | Mohora M, Greabu M, Alexandra T, et al. (2009) Redox-sensitive signaling factors and antioxidants. Farmacia 57: 399-411. |
[173] |
Hayden MS, Ghosh S (2004) Signaling to NF-kappaB. Genes Dev 18: 2195-2204. doi: 10.1101/gad.1228704
![]() |
[174] |
Kabe Y., Ando K, Hirao S, et al. (2005) Redox regulation of NFkappaB activation: distinctredox regulation between the cytoplasm and the nucleus. Antioxid.Redox Signal 7: 395-403. doi: 10.1089/ars.2005.7.395
![]() |
[175] | Sah SK, Reddy KR, Li J (2016). Abscisic acid and abiotic stress tolerance in crop plants. Front Plant Sci 7: 571. |
[176] |
Stone SL, Williams LA, Farmer LM, et al. (2006) KEEP ON GOING, a RING E3 ligase essential for Arabidopsis growth and development, is involved in abscisic acid signaling. Plant Cell 18: 3415-3428. doi: 10.1105/tpc.106.046532
![]() |
[177] |
Lyzenga WJ, Liu H, Schofield A, et al. (2013) Arabidopsis CIPK26 interacts with KEG, components of the ABA signalling network and is degraded by the ubiquitin-proteasome system. J Exp Bot 64: 2779-2791. doi: 10.1093/jxb/ert123
![]() |
[178] |
Dai M, Xue Q, Mccray T, et al. (2013) The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis. Plant Cell 25: 517-534. doi: 10.1105/tpc.112.105767
![]() |
[179] |
Miura K, Lee J, Jin JB, et al. (2009) Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc Natl Acad Sci USA 106: 5418-5423. doi: 10.1073/pnas.0811088106
![]() |
[180] | Xanthoudakis S, Curran T (1992) Identification and characterization of Ref-1, a nuclear protein that facilitates AP-1 DNA-binding activity. EMBO J 11: 653-665. |
[181] |
Hirota K, Matsui M, Iwata S, et al. (1997) AP-1 transcriptional activity is regulated by a direct association between thioredoxin and Ref-1. Proc Natl Acad Sci USA 94: 3633-3538. doi: 10.1073/pnas.94.8.3633
![]() |
[182] |
Després C, DeLong C, Glaze S, et al. (2000) The Arabidopsis NPR1/NIM1 protein enhances the DNA binding activity of a subgroup of the TGA family of bZIP transcription factors. Plant Cell 12: 279-290. doi: 10.1105/tpc.12.2.279
![]() |
[183] |
Zhang Y, Fan W, Kinkema M, et al. (1999) Interaction of NPR1 with basic leucine zipper transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene. Proc Natl Acad Sci USA 96: 6523-6528. doi: 10.1073/pnas.96.11.6523
![]() |
[184] |
Després C, Chubak C, Rochon A, et al. (2003) The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell 15: 2181-2191. doi: 10.1105/tpc.012849
![]() |
[185] |
Mou Z, Fan W, Dong X (2003) Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell 113: 935-944. doi: 10.1016/S0092-8674(03)00429-X
![]() |
[186] |
Tada Y, Spoel SH, Pajerowska-Mukhtar K, et al. (2008) Plant immunity requires conformational charges of NPR1 via S-nitrosylation and thioredoxins. Science 321: 952-956. doi: 10.1126/science.1156970
![]() |
[187] |
Lindermayr C, Sell S, Müller B, et al. (2010) Redox regulation of the NPR1-TGA1 system of Arabidopsis thaliana by nitric oxide. Plant Cell 22: 2894-2907. doi: 10.1105/tpc.109.066464
![]() |
[188] |
Xing S, Zachgo S (2008) ROXY1 and ROXY2, two Arabidopsis glutaredoxin genes, are required for anther development. Plant J 53: 790-801. doi: 10.1111/j.1365-313X.2007.03375.x
![]() |
[189] |
Li S, Gusche N, Zachgo S (2011) The ROXY1 C-terminal L**LL motif is essential for the interaction with TGA transcription factors. Plant Physiol 157: 2056-2068. doi: 10.1104/pp.111.185199
![]() |
[190] |
Heine FG, Hernandez JM, Grotewold E (2004) Two cysteines in plant R2R3 MYB domains participate in REDOX-dependent DNA binding. J Biol Chem 279: 37878-37885. doi: 10.1074/jbc.M405166200
![]() |
[191] |
Guehmann S, Vorbrueggen G, Kalkbrenner F, et al. (1992) Reduction of a conserved Cys is essential for Myb DNA-binding. Nucleic Acids Res 20: 2279-2286. doi: 10.1093/nar/20.9.2279
![]() |
[192] | Li S (2015) The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development. Plant Signal Behav 10: e1044192. |
[193] |
Viola IL, Güttlein LN , Gonzalez DH (2013) Redox modulation of plant developmental regulators from the class I TCP transcription factor family. Plant Physiol 162: 1434-1447. doi: 10.1104/pp.113.216416
![]() |
[194] |
Shaikhali J, Noren L, Barajas-Lopez JD, et al. (2012) Redox-mediated mechanisms regulate DNA-binding activity of the G-group of bZIP transcription factors in Arabidopsis. J Biol Chem 287: 27510-27525. doi: 10.1074/jbc.M112.361394
![]() |
[195] |
Jakoby M., Weisshaar B., Dröge-Laser W., et al. (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7: 106-111. doi: 10.1016/S1360-1385(01)02223-3
![]() |
[196] | Schindler U, Terzaghi W, Beckmann H, et al. (1992) DNA binding site preferences and transcriptional activation properties of the Arabidopsis transcription factor GBF1. EMBO J 11: 1275-1289. |
[197] |
Shen H, Cao K, Wang X (2008) AtbZIP16 and AtbZIP68, two new members of GBFs, can interact with other G group bZIPs in Arabidopsis thaliana. BMB Rep 41: 132-138. doi: 10.5483/BMBRep.2008.41.2.132
![]() |
[198] |
Kleine T, Kindgren P, Benedict C, et al. (2007) Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance. Plant Physiol 144: 1391-1406. doi: 10.1104/pp.107.098293
![]() |
[199] |
Hsieh WP, Hsieh HL, Wu SH (2012) Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development. Plant Cell 24: 3997-4011. doi: 10.1105/tpc.112.105478
![]() |
[200] |
Shaikhali J (2015) GIP1 protein is a novel cofactor that regulates DNA-binding affinity of redox-regulated members of bZIP transcription factors involved in the early stages of Arabidopsis development. Protoplasma 252: 867-883. doi: 10.1007/s00709-014-0726-9
![]() |
[201] | Lee HW, Park JH, Park MY, et al. (2014) GIP1 may act as a coactivator that enhances transcriptional activity of LBD18 in Arabidopsis. J Plant Physiol 171: 14-18. |
[202] |
Kelleher III RJ, Flanagan PM, Kornberg RD (1990) A novel mediator between activator proteins and the RNA polymerase II transcription apparatus. Cell 61: 1209-1215. doi: 10.1016/0092-8674(90)90685-8
![]() |
[203] |
Backstrom S, Elfving N, Nilsson R, et al. (2007) Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the MED25 subunit. Mol Cell 26: 717-729. doi: 10.1016/j.molcel.2007.05.007
![]() |
[204] |
Mathur S, Vyas S, Kapoor S, et al. (2011) The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. Plant Physiol 157: 1609-1627. doi: 10.1104/pp.111.188300
![]() |
[205] |
Cantin GT, Stevens JL, Berk AJ (2003) Activation domain-Mediator interactions promote transcription preinitiation complex assembly on promoter DNA. Proc Natl Acad Sci USA 100: 12003-12008. doi: 10.1073/pnas.2035253100
![]() |
[206] |
Wang G, Balamotis MA, Stevens JL, et al. (2005). Mediator requirement for both recruitment and postrecruitment steps in transcription initiation. Mol Cell 17: 683-694. doi: 10.1016/j.molcel.2005.02.010
![]() |
[207] |
Malik S, Barrero MJ, Jones T (2007) Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator. Proc Natl Acad Sci USA 104: 6182-6187. doi: 10.1073/pnas.0608717104
![]() |
[208] |
Takahashi H, Parmely TJ, Sato S, et al. (2011) Human Mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 146: 92-104. doi: 10.1016/j.cell.2011.06.005
![]() |
[209] |
Mukundan B, Ansari A (2011) Novel role for Mediator complex subunit Srb5/Med18 in termination of transcription. J Biol Chem 286: 37053-37057. doi: 10.1074/jbc.C111.295915
![]() |
[210] |
Kim YJ, Zheng B, Yu Y, et al. (2011) The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J 30: 814-822. doi: 10.1038/emboj.2011.3
![]() |
[211] |
Lai F, Orom UA, Cesaroni M, et al. (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494: 497-501. doi: 10.1038/nature11884
![]() |
[212] |
Cerdan PD, Chory J (2003) Regulation of flowering time by light quality. Nature 423: 881-885. doi: 10.1038/nature01636
![]() |
[213] |
Elfving N, Davoine C, Benlloch R, et al. (2011) The Arabidopsis thaliana Med25 mediator subunit integrates environmental cues to control plant development. Proc Natl Acad Sci USA 108: 8245-8250. doi: 10.1073/pnas.1002981108
![]() |
[214] |
Zhang X, Yao J, Zhang Y, et al. (2013) The Arabidopsis mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses. Plant J 75: 484-497. doi: 10.1111/tpj.12216
![]() |
[215] |
Zheng Z, Guan H, Leal F, et al. (2013) Mediator subunit18 controls flowering time and floral organ identity in Arabidopsis. PLoS One 8: e53924. doi: 10.1371/journal.pone.0053924
![]() |
[216] |
Klose C, Buche C, Fernandez AP, et al. (2012) The Mediator complex subunit PFT1 interferes with COP1 and HY5 in the regulation of Arabidopsis light-signaling. Plant Physiol 160: 289-307. doi: 10.1104/pp.112.197319
![]() |
[217] |
Cevik C, Kidd BN, Zhang P, et al. (2012) Mediator 25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis. Plant Physiol 160: 541-555. doi: 10.1104/pp.112.202697
![]() |
[218] |
Dhawan R, Luo H, Foerster AM, et al. (2009) HISTONE MONOUBIQUITINATION1 interacts with a subunit of the Mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis. Plant Cell 21: 1000-1019. doi: 10.1105/tpc.108.062364
![]() |
[219] | Wang C, Du X2, Mou Z (2016) The mediator complex subunits MED14, MED15, and MED16 are involved in defense signaling crosstalk in Arabidopsis. Front Plant Sci 7: 1947. |
[220] |
Fallath T, Kidd BN, Stiller J, et al. (2017) MEDIATOR18 and MEDIATOR20 confer susceptibility to Fusarium oxysporum in Arabidopsis thaliana. PLoS One 12: e0176022. doi: 10.1371/journal.pone.0176022
![]() |
[221] |
Gillmor CS, Park MY, Smith MR, et al. (2010) The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis. Development 137: 113-122. doi: 10.1242/dev.043174
![]() |
[222] |
Autran D, Jonak C, Belcram K, et al. (2002) Cell numbers and leaf development in Arabidopsis: a functional analysis of the STRUWWELPETER gene. EMBO J 21: 6036-6049. doi: 10.1093/emboj/cdf614
![]() |
[223] |
Kidd BN, Edgar CI, Kumar KK, et al. (2009) The mediator complex subunit PFT1 is a key regulator of jasmonate-dependent defense in Arabidopsis. Plant Cell 21: 2237-2252. doi: 10.1105/tpc.109.066910
![]() |
[224] |
Sundaravelpandian K, Chandrika NN, Schmidt W (2013) PFT1, a transcriptional Mediator complex subunit, controls root hair differentiation through reactive oxygen species (ROS) distribution in Arabidopsis. New Phytol 197: 151-161. doi: 10.1111/nph.12000
![]() |
[225] |
Zhang X, Wang C, Zhang Y, et al. (2012) The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways. Plant Cell 24: 4294-309. doi: 10.1105/tpc.112.103317
![]() |
[226] |
Fu ZQ, Dong X (2013) Systemic acquired resistance: turning local infection into global defense. Annu Rev Plant Biol 64: 839-863. doi: 10.1146/annurev-arplant-042811-105606
![]() |
[227] | Lai Z, Schluttenhofer CM, Bhide K, et al. (2014) MED18 interaction with distinct transcription factors regulates multiple plant functions. Nat Commun 5: 3064. |
[228] |
Shaikhali J, Davoine C, Brännström K, et al. (2015) Biochemical and redox characterization of the mediator complex and its associated transcription factor GeBPL, a GLABROUS1 enhancer binding protein. Biochem J 468: 385-400. doi: 10.1042/BJ20150132
![]() |
[229] |
Shaikhali J, Davoine C, Björklund B, et al. (2016) Redox regulation of the MED28 and MED32 mediator subunits is important for development and senescence. Protoplasma 253: 957-963. doi: 10.1007/s00709-015-0853-y
![]() |
[230] | Shaikhali J, Rouhier N, Hecker A, et al. (2017) Covalent and non-covalent associations mediate MED28 homo-oligomerization. J Plant Biochem Physiol 5: 1-5. |
[231] |
Cao H, Bowling SA, Gordon AS, et al. (1994) Characterization of an Arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance. Plant Cell 6: 1583-1592. doi: 10.1105/tpc.6.11.1583
![]() |
[232] |
Zhang Y, Tessaro MJ, Lassner M, et al. (2003) Knock-out analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance. Plant Cell 15: 2647-2653. doi: 10.1105/tpc.014894
![]() |
[233] |
Kuge S, Arita M, Murayama A, et al. (2001) Regulation of the yeast Yap1 nuclear export signal is mediated by redox signal-induced reversible disulfide bond formation. Mol Cell Biol 21: 6139-6150. doi: 10.1128/MCB.21.18.6139-6150.2001
![]() |
[234] |
Zhang X, Wang C, Zhang Y (2012) The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways. Plant Cell 24: 4294-4309. doi: 10.1105/tpc.112.103317
![]() |
[235] |
Bachi A, Dalle-Donne I, Scaloni A (2013) Redox proteomics: chemical principles, methodological approaches and biological/biomedical promises. Chem Rev 113: 596-698. doi: 10.1021/cr300073p
![]() |
[236] |
Mock HP, Dietz KJ (2016) Redox proteomics for the assessment of redox-related posttranslational regulation in plants. Biochim Biophys Acta 1864: 967-73. doi: 10.1016/j.bbapap.2016.01.005
![]() |
[237] |
Butterfield DA, Perluigi M (2017) Redox Proteomics: A Key Tool for New Insights into Protein Modification with Relevance to Disease. Antioxid Redox Signal 26: 277-279. doi: 10.1089/ars.2016.6919
![]() |
[238] |
Butterfield DA, Gu L, Di Domenico F, et al. (2014) Mass spectrometry and redox proteomics: applications in disease. Mass Spectrom Rev 33: 277-301. doi: 10.1002/mas.21374
![]() |
[239] |
Erhardt M, Adamska I, Franco OL (2010) Plant nuclear proteomics--inside the cell maestro. FEBS J 277: 3295-3307. doi: 10.1111/j.1742-4658.2010.07748.x
![]() |
[240] | Narula K, Datta A, Chakraborty N, et al. (2013) Comparative analyses of nuclear proteome: extending its function. Front Plant Sci 4: 100. |
[241] |
Petrovská B, Šebela M, Doležel J (2015) Inside a plant nucleus: discovering the proteins. J Exp Bot 66: 1627-1640. doi: 10.1093/jxb/erv041
![]() |
[242] |
Holtgrefe S, Gohlke J, Starmann J, et al. (2008) Regulation of plant cytosolic glyceraldehyde 3 phosphate dehydrogenase isoforms by thiol modifications. Physiol Plant 133: 211-228. doi: 10.1111/j.1399-3054.2008.01066.x
![]() |
[243] |
Tavares CP, Vernal J, Delena RA, et al. (2014) S-nitrosylation influences the structure and DNA binding activity of AtMYB30 transcription factor from Arabidopsis thaliana. BBA Proteins Proteomics 1844: 810-817. doi: 10.1016/j.bbapap.2014.02.015
![]() |
[244] |
Chaki M, Shekariesfahlan A, Ageeva A, et al. (2015) Identification of nuclear target proteins for S-nitrosylation in pathogen-treated Arabidopsis thaliana cell cultures. Plant Sci 238: 115-126. doi: 10.1016/j.plantsci.2015.06.011
![]() |
[245] |
Calderóna A, Ortiz-Espína A, Iglesias-Fernándezb R, et al. (2017) Thioredoxin (Trxo1) interacts with proliferating cell nuclear antigen (PCNA) and its overexpression affects the growth of tobacco cell culture. Redox Biol 11: 688-700. doi: 10.1016/j.redox.2017.01.018
![]() |
[246] |
Verrastro I, Pasha S, Jensen KT, et al. (2015) Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules 5: 378-411. doi: 10.3390/biom5020378
![]() |
[247] |
Boronat S, Domènech A, Hidalgo E (2017) Proteomic characterization of reversible thiol oxidations in proteomes and proteins. Antioxid Redox Signal 26: 329-344. doi: 10.1089/ars.2016.6720
![]() |
1. | Luis F. Muñoz-Pérez, J.E. Macías-Díaz, An implicit and convergent method for radially symmetric solutions of Higgs' boson equation in the de Sitter space–time, 2021, 165, 01689274, 270, 10.1016/j.apnum.2021.02.018 | |
2. | M. Briani, G. Puppo, M. Ribot, Angle dependence in coupling conditions for shallow water equations at channel junctions, 2022, 108, 08981221, 49, 10.1016/j.camwa.2021.12.021 | |
3. | Aidan Hamilton, Jing-Mei Qiu, Hong Zhang, 2023, Scalable Riemann Solvers with the Discontinuous Galerkin Method for Hyperbolic Network Simulation, 9798400701900, 1, 10.1145/3592979.3593421 |