Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors
Phylogenetic analysis of the phytochrome superfamily reveals distinct microbial subfamilies of photoreceptors
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DOI：
10.1042/bj20050826
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发表时间：
2005-11-15
影响因子：
4.1
通讯作者：
Vierstra, RD
中科院分区：
文献类型：
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作者：
Karniol, B;Wagner, JR;Vierstra, RD
PHY(光敏变色剂)是光致变色光感受器的超家族，它利用毕林型发色团来感知红光和远红光。虽然最初被认为仅限于植物，但现在积累的遗传和基因组分析表明，它们在微生物中也很普遍。通过系统发育和生化研究的结合，我们扩展了Phy超家族，并将其成员组织成不同的功能分支，包括Phy(植物Phys)、Bphps(细菌植物色素)、Cphs(蓝藻Phys)、Fphs(真菌Phys)和一系列Phy-like序列。它们都含有一个标志性的GAF(cGMP磷酸二酯酶/腺苷环化酶/FHIA)结构域，它包含胆碱裂解酶的活性。帮助稳定PFR形式(Phy的远红光吸收形式)的PHY结构域(具体使用大写字母表示PHY结构域)在除Phy-like序列之外的所有GAF区域的下游。PHY、CPH、BphP和FPH家族还包括GAF结构域上游的PLD[N-末端PAS(PER/AMT/Sim)样结构域]。GAF和PLD基序中保守残基的定点突变支持了它们在生色团结合和/或光谱活性中的重要性。与Lamparter，Carrascal，Michael，Martinez，Rottwinkel和Abian[(2004)BioChemical 43,3659-3669]一致，几个BphP的PLD中保守的半胱氨酸被发现是通过C-3乙烯基侧链与BlinA环上的发色团结合所必需的。在耐辐射放线杆菌和从海洋和极端酸性环境中获得的微生物中也发现了PHY类型的序列，从而进一步扩大了这些光感受器的范围。根据它们的组织和分布，提出了Phy超家族进化为不同的光感受器类型。
Phys (phytochromes) are a superfamily of photochromic photo-receptors that employ a bilin-type chromophore to sense red and far-red light. Although originally thought to be restricted to plants, accumulating genetic and genomic analyses now indicate that they are also prevalent among micro-organisms. By a combination of phylogenetic and biochemical studies, we have expanded the Phy superfamily and organized its members into distinct functional clades which include the phys (plant Phys), BphPs (bacteriophytochromes), Cphs (cyanobacterial Phys), Fphs (fungal Phys) and a collection of Phy-like sequences. All contain a signature GAF (cGMP phosphodiesterase/adenylate cyclase/FhIA) domain, which houses the bilin lyase activity. A PHY domain (uppercase letters are used to denote the PHY domain specifically), which helps stabilize the Pfr form (far-red-light-absorbing form of Phy), is downstream of the GAF region in all but the Phy-like sequences. The phy, Cph, BphP and Fph families also include a PLD [N-terminal PAS (Per/Amt/Sim)-like domain] upstream of the GAF domain. Site-directed mutagenesis of conserved residues within the GAF and PLD motifs supports their importance in chromophore binding and/or spectral activity. In agreement with Lamparter, Carrascal, Michael, Martinez, Rottwinkel and Abian [(2004) Biochemistry 43, 3659-3669], a conserved cysteine within the PLD of several BphPs was found to be necessary for binding the chromophore via the C-3 vinyl side chain on the bilin A ring. Phy-type sequences were also discovered in the actinobacterium Kineococcus radiotolerans and collections of microorganisms obtained from marine and extremely acidic environments, thus expanding further the range of these photoreceptors. Based on their organization and distribution, the evolution of the Phy superfamily into distinct photoreceptor types is proposed.