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author:("Lin, chennai")
1.  Phytochromes and Phytohormones: The Shrinking Degree of Separation 
Molecular Plant  2012;6(1):5-7.
doi:10.1093/mp/sss102
PMCID: PMC3612011  PMID: 22973064
2.  Multiple bHLH Proteins form Heterodimers to Mediate CRY2-Dependent Regulation of Flowering-Time in Arabidopsis 
PLoS Genetics  2013;9(10):e1003861.
Arabidopsis thaliana cryptochrome 2 (CRY2) mediates light control of flowering time. CIB1 (CRY2-interacting bHLH 1) specifically interacts with CRY2 in response to blue light to activate the transcription of FT (Flowering Locus T). In vitro, CIB1 binds to the canonical E-box (CACGTG, also referred to as G-box) with much higher affinity than its interaction with non-canonical E-box (CANNTG) DNA sequences. However, in vivo, CIB1 binds to the chromatin region of the FT promoter, which only contains the non-canonical E-box sequences. Here, we show that CRY2 also interacts with at least CIB5, in response to blue light, but not in darkness or in response to other wavelengths of light. Our genetic analysis demonstrates that CIB1, CIB2, CIB4, and CIB5 act redundantly to activate the transcription of FT and that they are positive regulators of CRY2 mediated flowering. More importantly, CIB1 and other CIBs proteins form heterodimers, and some of the heterodimers have a higher binding affinity than the CIB homodimers to the non-canonical E-box in the in vitro DNA-binding assays. This result explains why in vitro CIB1 and other CIBs bind to the canonical E-box (G-box) with a higher affinity, whereas they are all associated with the non-canonical E-boxes at the FT promoter in vivo. Consistent with the hypothesis that different CIB proteins play similar roles in the CRY2-midiated blue light signaling, the expression of CIB proteins is regulated specifically by blue light. Our study demonstrates that CIBs function redundantly in regulating CRY2-dependent flowering, and that different CIBs form heterodimers to interact with the non-canonical E-box DNA in vivo.
Author Summary
Arabidopsis thaliana blue light receptor cryptochromes (CRYs) mediate light control of flowering time by interacting with CIB1 (CRY2-interacting bHLH1) in response to blue light. However, it remains unclear how the blue light-dependent CRY2-CIB1 interaction affects the FT transcription. We report here that in addition to CIB1, CRY2 also interact with CIB1 related bHLH proteins, CIBs. These CIBs act redundantly with CIB1 to activate the transcription of FT and flowering. More importantly, CIB1 and the CIBs can form heterodimers and some of those heterodimers have a higher binding affinity to the non-canonical E-box, although their homodimers all prefer canonical E-box (G-box), so they can bind to the non-canonical E-Box sequences of the FT promoter. This is the first example in plants that heterodimerization of bHLH can change the DNA binding affinity or specificity. CIB proteins are involved in blue light signaling and they are specifically stabilized by blue light.
doi:10.1371/journal.pgen.1003861
PMCID: PMC3794922  PMID: 24130508
3.  CONSTANS-LIKE 7 regulates branching and shade avoidance response in Arabidopsis  
Journal of Experimental Botany  2013;64(4):1017-1024.
Branching is an important trait of plant development regulated by environmental signals. Phytochromes in Arabidopsis mediate branching in response to the changes in the red light:far-red light ratio (R:FR), the mechanisms of which are still elusive. Here it is shown that overexpression of CONSTANS-LIKE 7 (COL7) results in an abundant branching phenotype which could be efficiently suppressed by shade or a simulated shade environment (low R:FR). Moreover, col7 mutants develop shorter hypocotyls and COL7 overexpression lines develop longer hypocotyls in comparison with the wild type in low R:FR, indicating that COL7 acts as an enhancer of the shade avoidance response. In shade or transient low R:FR, transcriptional and post-transcriptional expression levels of COL7 are up-regulated and positively associated with rapid mRNA accumulation of PHYTOCHROME INTERACTING FACTOR 3-LIKE 1 (PIL1), a marker gene of shade avoidance syndrome (SAS). Taken together, the results suggest a dual role for COL7 which promotes branching in high R:FR conditions but enhances SAS in low R:FR conditions.
doi:10.1093/jxb/ers376
PMCID: PMC3580813  PMID: 23314820
Branching; COL7; light signal transduction; phytochrome B; PIL1; shade avoidance response.
4.  The action mechanisms of plant cryptochromes 
Trends in Plant Science  2011;16(12):684-691.
The blue light receptors cryptochromes mediate various light responses in plants. The photoexcited cryptochrome molecules undergo a number of biophysical and biochemical changes, including electron transfer, phosphorylation, and ubiquitination, resulting in conformational changes to propagate light signals. Two modes of cryptochrome signal transduction have been recently discovered, the CIB (cryptochrome-interacting basic-helix-loop-helix 1)-dependent CRY2 regulation of transcription and the SPA1/COP1 (SUPPRESSOR OF PHYA /CONSTITUTIVELY PHOTOMORPHOGENIC1)-dependent cryptochrome regulation of proteolysis. Both cryptochrome signaling pathways rely on blue light-dependent interactions between the cryptochrome photoreceptor and its signaling proteins to modulate gene expression changes in response to blue light, leading to altered developmental programs of plants.
doi:10.1016/j.tplants.2011.09.002
PMCID: PMC3277817  PMID: 21983106
5.  Optogenetic Control of Transcription in Zebrafish 
PLoS ONE  2012;7(11):e50738.
Light inducible protein-protein interactions are powerful tools to manipulate biological processes. Genetically encoded light-gated proteins for controlling precise cellular behavior are a new and promising technology, called optogenetics. Here we exploited the blue light-induced transcription system in yeast and zebrafish, based on the blue light dependent interaction between two plant proteins, blue light photoreceptor Cryptochrome 2 (CRY2) and the bHLH transcription factor CIB1 (CRY-interacting bHLH 1). We demonstrate the utility of this system by inducing rapid transcription suppression and activation in zebrafish.
doi:10.1371/journal.pone.0050738
PMCID: PMC3511356  PMID: 23226369
6.  INCREASED ANGIOTENSIN II INDUCED HYPERTENSION AND INFLAMMATORY CYTOKINES IN MICE LACKING ANGIOTENSIN CONVERTING ENZYME N DOMAIN ACTIVITY 
Hypertension  2011;59(2):283-290.
Angiotensin converting enzyme (ACE) is composed of the N- and C-terminal catalytic domains. To study the role of the ACE domains in the inflammatory response, N-KO and C-KO mice, models lacking one of the two ACE domains, were analyzed during angiotensin II-induced hypertension. At 2 weeks, N-KO mice have systolic blood pressures that averaged 173 ± 4.6 mm Hg, which is more than 25 mm Hg higher than the blood pressures observed in wild-type or C-KO mice (146 ± 3.2 and 147 ± 4.2 mm Hg). After 3 weeks, blood pressure differences between N-KO, C-KO and WT were even more pronounced. Macrophages from N-KO mice have increased expression of tumor necrosis factor α after stimulation with either lipopolysaccharide (about 4-fold) or angiotensin II (about 2-fold), as compared to C-KO or wild-type mice. Inhibition of the enzyme prolyl oligopeptidase, responsible for the formation of acetyl SDKP and other peptides, eliminated the blood pressure difference and the difference in tumor necrosis factor α expression between angiotensin II treated N-KO and wild-type mice. However, this appears independent of acetyl SDKP. These data establish significant differences in the inflammatory response as a function of ACE N- or C-domain catalytic activity. They also indicate a novel role of prolyl oligopeptidase in the cytokine regulation and in the blood pressure response to experimental hypertension.
doi:10.1161/HYPERTENSIONAHA.111.180844
PMCID: PMC3266456  PMID: 22203735
Angiotensin converting enzyme; hypertension; angiotensin II; prolyl oligopeptidase; acetyl SDKP
7.  The carboxypeptidase angiotensin converting enzyme (ACE) shapes the MHC class I peptide repertoire 
Nature Immunology  2011;12(11):1078-1085.
The surface presentation of peptides by major histocompatibility complex (MHC) class I molecules is critical to CD8+ T cell mediated adaptive immune responses. Aminopeptidases are implicated in the editing of peptides for MHC class I loading, but C-terminal editing is thought due to proteasome cleavage. By comparing genetically deficient, wild-type and over-expressing mice, we now identify the dipeptidase angiotensin-converting enzyme (ACE) as playing a physiologic role in peptide processing for MHC class I. ACE edits the C-termini of proteasome-produced class I peptides. The lack of ACE exposes novel antigens but also abrogates some self-antigens. ACE has major effects on surface MHC class I expression in a haplotype-dependent manner. We propose a revised model of MHC class I peptide processing by introducing carboxypeptidase activity.
doi:10.1038/ni.2107
PMCID: PMC3197883  PMID: 21964607
8.  Searching for a photocycle of the cryptochrome photoreceptors 
Current opinion in plant biology  2010;13(5):578-586.
The initial photochemistry of plant cryptochromes has been extensively investigated in recent years. It is hypothesized that cryptochrome photoexcitation involves a Trp-triad-dependent photoreduction. According to this hypothesis, cryptochromes in the resting state contain oxidized FAD; light triggers a sequential electron transfer from three tryptophan residues to reduce FAD to a neutral semiquinone (FADH•); FADH• is the presumed signaling state and it is re-oxidized to complete the photocycle. However, this photoreduction hypothesis is currently under debate. An alternative model argues that the initial photochemistry of cryptochromes involves a photolyase-like cyclic electron shuttle without a bona fide redox reaction mediated by the Trp-triad residues, leading to conformational changes, signal propagation, and physiological responses.
doi:10.1016/j.pbi.2010.09.005
PMCID: PMC2972227  PMID: 20943427
9.  The Cryptochrome Blue Light Receptors 
Cryptochromes are photolyase-like blue light receptors originally discovered in Arabidopsis but later found in other plants, microbes, and animals. Arabidopsis has two cryptochromes, CRY1 and CRY2, which mediate primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, respectively. In addition, cryptochromes also regulate over a dozen other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Cryptochromes have two domains, the N-terminal PHR (Photolyase-Homologous Region) domain that bind the chromophore FAD (flavin adenine dinucleotide), and the CCE (CRY C-terminal Extension) domain that appears intrinsically unstructured but critical to the function and regulation of cryptochromes. Most cryptochromes accumulate in the nucleus, and they undergo blue light-dependent phosphorylation or ubiquitination. It is hypothesized that photons excite electrons of the flavin molecule, resulting in redox reaction or circular electron shuttle and conformational changes of the photoreceptors. The photoexcited cryptochrome are phosphorylated to adopt an open conformation, which interacts with signaling partner proteins to alter gene expression at both transcriptional and posttranslational levels and consequently the metabolic and developmental programs of plants.
PMCID: PMC3155252  PMID: 21841916
10.  Blue Light-Dependent Interaction of CRY2 with SPA1 Regulates COP1 activity and Floral Initiation in Arabidopsis 
Current biology : CB  2011;21(10):841-847.
Summary
Cryptochromes are blue light receptors that mediate light regulation of gene expression in all major evolution lineages, but the molecular mechanism underlying cryptochrome signal transduction remains not fully understood [1, 2]. It has been reported that cryptochromes suppress activity of the multifunctional E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) to regulate gene expression in response to blue light [3, 4]. But how plant cryptochromes mediate light suppression of COP1 activity remains unclear. We report here that Arabidopsis CRY2 (cryptochrome 2) undergoes blue light-dependent interaction with the COP1-interacting protein SUPPRESSOR OF PHYTOCHROME A 1 (SPA1) [5, 6]. We demonstrate that SPA1 acts genetically downstream from CRY2 to mediate blue light suppression of the COP1-dependent proteolysis of the flowering-time regulator CONSTANS (CO) [7, 8]. We further show that blue light-dependent CRY2-SPA1 interaction stimulates CRY2-COP1 interaction. These results reveal for the first time a wavelength-specific mechanism by which a cryptochrome photoreceptor mediates light regulation of protein degradation to modulate developmental timing in Arabidopsis.
doi:10.1016/j.cub.2011.03.048
PMCID: PMC3150455  PMID: 21514160
11.  The Cryptochrome Blue Light Receptors 
Cryptochromes are photolyase-like blue light receptors originally discovered in Arabidopsis but later found in other plants, microbes, and animals. Arabidopsis has two cryptochromes, CRY1 and CRY2, which mediate primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, respectively. In addition, cryptochromes also regulate over a dozen other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Cryptochromes have two domains, the N-terminal PHR (Photolyase-Homologous Region) domain that bind the chromophore FAD (flavin adenine dinucleotide), and the CCE (CRY C-terminal Extension) domain that appears intrinsically unstructured but critical to the function and regulation of cryptochromes. Most cryptochromes accumulate in the nucleus, and they undergo blue light-dependent phosphorylation or ubiquitination. It is hypothesized that photons excite electrons of the flavin molecule, resulting in redox reaction or circular electron shuttle and conformational changes of the photoreceptors. The photoexcited cryptochrome are phosphorylated to adopt an open conformation, which interacts with signaling partner proteins to alter gene expression at both transcriptional and posttranslational levels and consequently the metabolic and developmental programs of plants.
doi:10.1199/tab.0135
PMCID: PMC3155252  PMID: 21841916
12.  Tissue Specific Expression of Angiotensin Converting Enzyme: A new way to study an old friend 
International immunopharmacology  2008;8(2):171-176.
Angiotensin-converting enzyme (ACE) plays a central role in blood pressure regulation by producing the vasoconstrictor angiotensin II. When ACE knockout mice were studied, they presented with a complicated phenotype, including cardiovascular, reproductive, hematologic and developmental defects. The complexity of an ACE knockout mouse emphasizes the advantages and disadvantages of the classic knockout strategy. An animal lacking all ACE is very different from a wild type animal, and can be modeled as representing an extreme phenotype. To understand the role of ACE in a tissue and organ specific fashion, our group used targeted homologous recombination to create mouse models in which a promoter swapping strategy results in very restricted tissue patterns of ACE expression. Mice with ACE expression only in the heart, termed ACE 8/8 mice, present with atria enlargement and electrical conduction defects, but normal ventricular function. Mice with ACE expression only in monocytes and macrophages, termed ACE 10/10 mice, have a marked resistance to the growth of melanoma due to an enhanced immune response characterized by increased tumor specific CD8+ T cells and increased proinflammatory cytokines. These mice may define a new means of augmenting the immune response, potentially useful in human clinical situations. The promoter swapping strategy permits scientific investigation of questions unapproachable by other experimental approaches.
doi:10.1016/j.intimp.2007.08.010
PMCID: PMC2247367  PMID: 18182222
13.  A photoreceptor going nowhere but the nucleus 
Plant Signaling & Behavior  2008;3(5):331-332.
Cryptochrome 2 (CRY2) is a blue/UV-A light receptor that regulates light inhibition of cell elongation and photoperiodic promotion of floral initiation in Arabidopsis. We and others have previously shown that CRY2 is a nuclear protein that regulates gene expression to affect plant development. We also showed that CRY2 is phosphorylated in response to blue light and the phosphorylated CRY2 is most likely active and degraded in blue light. Given that protein translation (and probably chromophore attachment) takes place in the cytosol and that a photoreceptor would absorb photon instantaneously, it would be interesting to know where those inter-connected events occur in the cell. Our results showed that freshly synthesized CRY2 photoreceptor is inactive in the cytosol although it may be photon-excited, it is imported into the nucleus where the photoreceptor is phosphorylated, performs its function, becomes ubiquitinated, and eventually gets degraded (Fig. 1).1 To our knowledge, this is the first example in any organism that a photoreceptor is shown to complete its post-translational life cycle in a single subcellular compartment.
PMCID: PMC2634274  PMID: 19841662
blue light; cryptochrome; ubiquitination; phosphorylation; Arabidopsis
14.  The cryptochromes 
Genome Biology  2005;6(5):220.
Cryptochromes are photoreceptors that regulate entrainment of the circadian clock by light in plants and animals. They are related to DNA photolyases and have similar three-dimensional structures, characterized by a α/β domain and a helical domain and including a chromophore, flavin adenine dinucleotide.
Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes are probably the evolutionary descendents of DNA photolyases, which are light-activated DNA-repair enzymes, and are classified into three groups - plant cryptochromes, animal cryptochromes, and CRY-DASH proteins. Cryptochromes and photolyases have similar three-dimensional structures, characterized by an α/β domain and a helical domain. The structure also includes a chromophore, flavin adenine dinucleotide (FAD). The FAD-access cavity of the helical domain is the catalytic site of photolyases, and it is predicted also to be important in the mechanism of cryptochromes.
doi:10.1186/gb-2005-6-5-220
PMCID: PMC1175950  PMID: 15892880

Results 1-14 (14)