Abstract
The PAS domains are signal modules, which are widely distributed in proteins across all kingdoms of life. They are common in photoreceptors and transcriptional regulators of eukaryotic circadian clocks q(bHLH-PAS proteins and PER in animals; PHY and ZTL in plants; and WC-1, 2, and VVD in fungi) and possess mainly protein–protein interaction and light-sensing functions. We conducted several evolutionary analyses of the PAS superfamily. Although the whole superfamily evolved primarily under strong purifying selection (average ω ranges from 0.0030 to 0.1164), some lineages apparently experienced strong episodic positive selection at some periods of the evolution. Although the PAS domains from different proteins vary in sequence and length, but they maintain a fairly conserved 3D structure, which is determined by only eight residues. The WC-1 and WC- 2, bHLH-PAS, and P er genes probably originated in the Neoproterozoic Era (1000–542 Mya), plant P hy and ZTL evolved in the Paleozoic (541–252 Mya), which might be a result of adaptation to the major climate and global light regime changes having occurred in those eras.
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This study was supported by The University of Hong Kong PhD Fellowship to Mr. Qiming Mei.
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Table S1
List of circadian genes containing PAS domain in this study (DOCX 103 kb)
Table S2
List of RPB2 sequences (DOC 156 kb)
Table S3
Results of the functional divergence analysis (DOCX 36 kb)
Figure S1
Unrooted maximum-likelihood tree of the bHLH-PAS proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.1 substitutions per site. (TIFF 881 kb)
High-resolution image
(JPEG 240 kb)
Figure S2
Unrooted maximum-likelihood tree of the PER proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.1 substitutions per site. (TIFF 576 kb)
High-resolution image
(JPEG 148 kb)
Figure S3
Unrooted maximum-likelihood tree of the ZTL proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.1 substitutions per site. (TIFF 440 kb)
High-resolution image
(JPEG 101 kb)
Figure S4
Maximum-likelihood tree of the PHY proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.1 substitutions per site. The phytochrome of Aspergillus terreus (AspeP, XP_001216524) was used as the outgroup. (TIFF 548 kb)
High-resolution image
(JPEG 132 kb)
Figure S5
Unrooted maximum-likelihood tree of the WC-1 proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.2 substitutions per site. (TIFF 319 kb)
High-resolution image
(JPEG 66 kb)
Figure S6
Unrooted maximum-likelihood tree of the WC-2 proteins. The values are the likelihoods and bootstraps, respectively. The values of the aLRT/bootstrap support below 0.5/50 are not shown. The branches having experienced episodic positive selection according to the PAML results (branch model = 1) are labeled with the respective d N/d S values. The bar below the tree indicates 0.2 substitutions per site. (TIFF 329 kb)
High-resolution image
(JPEG 66 kb)
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Mei, Q., Dvornyk, V. Evolution of PAS domains and PAS-containing genes in eukaryotes. Chromosoma 123, 385–405 (2014). https://doi.org/10.1007/s00412-014-0457-x
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DOI: https://doi.org/10.1007/s00412-014-0457-x