Structure and Signaling Mechanism of Per-ARNT-Sim Domains

Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith

doi:10.1016/j.str.2009.08.011

Cited by 476 publications

(670 citation statements)

References 74 publications

(146 reference statements)

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“…In addition to several sequence and functional homologs in other fungi, the LOV/PAS domain found in VVD and WC-1 is widespread and functionally conserved in different kingdoms (27,(43)(44)(45)(46)(47)(48). For instance, LOV domains from phototropins and FKF1 in Arabidopsis are still able to sense blue light when incorporated in Neurospora photoreceptor proteins (49).…”

Section: Discussionmentioning

confidence: 99%

Physical interaction between VIVID and white collar complex regulates photoadaptation inNeurospora

Chen¹,

DeMay

Gladfelter

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

137

166

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Photoadaptation, the ability to attenuate a light response on prolonged light exposure while remaining sensitive to escalating changes in light intensity, is essential for organisms to decipher time information appropriately, yet the underlying molecular mechanisms are poorly understood. In Neurospora crassa, VIVID (VVD), a small LOV domain containing blue-light photoreceptor protein, affects photoadaptation for most if not all light-responsive genes. We report that there is a physical interaction between VVD and the white collar complex (WCC), the primary blue-light photoreceptor and the transcription factor complex that initiates light-regulated transcriptional responses in Neurospora. Using two previously characterized VVD mutants, we show that the level of interaction is correlated with the level of WCC repression in constant light and that even lightinsensitive VVD is sufficient partly to regulate photoadaptation in vivo. We provide evidence that a functional GFP-VVD fusion protein accumulates in the nucleus on light induction but that nuclear localization of VVD does not require light. Constitutively expressed VVD alone is sufficient to change the dynamics of photoadaptation. Thus, our results demonstrate a direct molecular connection between two of the most essential light signaling components in Neurospora, VVD and WCC, illuminating a previously uncharacterized process for light-sensitive eukaryotic cells.light | white collar-1 | white collar-2 | photoreceptor | LOV domain

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Section: Discussionmentioning

confidence: 99%

Physical interaction between VIVID and white collar complex regulates photoadaptation inNeurospora

Chen¹,

DeMay

Gladfelter

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

137

166

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“…PAS is an acronym for Per (period circadian protein), Armt (Ah receptor nuclear translocator protein and Sim (single-minded protein) (Moglich et al 2009). PAS domains serve as sensors of diverse environmental stimuli and those with heme-binding pockets represent the most common sensing strategy for detecting changes in concentrations of oxygen, carbon monoxide or nitric oxide.…”

Section: The Pas Domain Of Hpk2mentioning

confidence: 99%

Gene Regulation, Two Component Regulatory Systems, and Adaptive Responses in Treponema Denticola

Marconi

2017

Current Topics in Microbiology and Immunology

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“…For example, the PAS protein NifA has been shown to respond to O 2 via a flavin adenine dinucleotide (FAD) (6), and the E. coli Dos protein (EcDos) is a heme-containing gas sensor that has N-terminal PAS domains (12). PAS domain families comprise a protein clan with divergent sequences (15); however, a recent study characterized the structures of PAS domains with known and unknown cofactors and showed a broadly conserved structure that is comprised of a five-stranded antiparallel ␤-sheet and several ␣-helices for all PAS domains characterized to date (34). The NifL sensor has been shown to be a reversible, FADbased O 2 /redox sensor that helps control the expression of nitrogen fixation genes in Azotobacter (21,26).…”

Section: Resultsmentioning

confidence: 99%

“…The I-Tasser model for the SO3389 PAS1/2 domains had a C score of 0.8, a TM score of 0.7 Ϯ 0.1, and an experimental RMSD (root mean square deviation) of 5.6 Ϯ 3.5 (positive C scores and TM scores of Ͼ0.5 indicate models with correct topology) (43). Moglich et al (34) used z scores from structural superpositions to construct a dendrogram based upon the degree of structural diversity between PAS domains from different proteins, and PAS domains with known cofactors (i.e., FMN, FAD, and heme) formed separate clusters. Therefore, we compared the predicted model of SO3389 PAS1/2 to known PAS sensors to gain insight into possible functions of SO3389 in conjunction with the presented phenotypic data.…”

Section: Resultsmentioning

confidence: 99%

“…The Pfam database (version 24.0) reports 33,313 sequences classified in the PAS protein clan, which contains 7 families, and the PAS and PAC motifs adopt a single globular fold of approximately 100 residues now known as the PAS domain (34). PAS domains are observed in all three domains of life, including metazoans, in which the domains can be part of hypoxia-inducible factors that play important roles in anaerobic metabolism, oxygen delivery, and angiogenesis (46).…”

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confidence: 99%

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Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth

Sundararajan

Kurowski

Yan

et al. 2011

Appl Environ Microbiol

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Although little is known of potential function for conserved signaling proteins, it is hypothesized that such proteins play important roles to coordinate cellular responses to environmental stimuli. In order to elucidate the function of a putative sensory box protein (PAS domains) in Shewanella oneidensis MR-1, the physiological role of SO3389 was characterized. The predicted open reading frame (ORF) encodes a putative sensory box protein that has PAS, GGDEF, and EAL domains, and an in-frame deletion mutant was constructed (⌬SO3389) with approximately 95% of the ORF deleted. Under aerated conditions, wild-type and mutant cultures had similar growth rates, but the mutant culture had a lower growth rate under static, aerobic conditions. Oxygen consumption rates were lower for mutant cultures (1.5-fold), and wild-type cultures also maintained lower dissolved oxygen concentrations under aerated growth conditions. When transferred to anoxic conditions, the mutant did not grow with fumarate, iron(III), or dimethyl sulfoxide (DMSO) as electron acceptors. Biochemical assays demonstrated the expression of different c-type cytochromes as well as decreased fumarate reductase activity in the mutant transferred to anoxic growth conditions. Transcriptomic studies showed the inability of the mutant to up-express and down-express genes, including c-type cytochromes (e.g., SO4047/SO4048, SO3285/SO3286), reductases (e.g., SO0768, SO1427), and potential regulators (e.g., SO1329). The complemented strain was able to grow when transferred from aerobic to anoxic growth conditions with the tested electron acceptors. The modeled structure for the SO3389 PAS domains was highly similar to the crystal structures of FAD-binding PAS domains that are known O 2 /redox sensors. Based on physiological, genomic, and bioinformatic results, we suggest that the sensory box protein, SO3389, is an O 2 /redox sensor that is involved in optimization of aerobic growth and transitions to anoxia in S. oneidensis MR-1.In the postgenomic era, uncharacterized genes pose a major challenge in biology (16), and many sequenced genomes still contain a large fraction (up to 30 to 40%) of genes without defined physiological roles (13). In fact, many aspects of signaling and stress response most likely reside in this fraction of genes for a given organism and underlie the lack of understanding in physiological responses and control of metabolism. Many uncharacterized genes/proteins are classified as sensory box proteins based upon conserved domains, but signals and cellular responses for most presumptive sensory box proteins are not known.Shewanella oneidensis MR-1, a facultative anaerobe classified as a gammaproteobacterium, can utilize numerous inorganic compounds as electron acceptors (e.g., oxygen, nitrate, and metals). The S. oneidensis MR-1 genome sequence was determined (20), and the most recent annotation of the 5.1-Mb genome estimated 4,467 genes, of which 1,623 had hypothetical functions (28). Many bacteria considered to be "environmental" organisms typica...

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Structure and Signaling Mechanism of Per-ARNT-Sim Domains

Cited by 476 publications

References 74 publications

Physical interaction between VIVID and white collar complex regulates photoadaptation inNeurospora

Physical interaction between VIVID and white collar complex regulates photoadaptation inNeurospora

Gene Regulation, Two Component Regulatory Systems, and Adaptive Responses in Treponema Denticola

Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth

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