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It should be noted that although a covalent adduct can theoretically form between a flavin and noncysteine residue, the key cysteine is considered obligate here to maintain consistency with the best characterized form of the LOV photocycle.) Sequence logos for motifs 1 and 2, identified by the MEME tool for a training set of 18 LOV proteins validated to photocycle, with the cysteine that forms the cysteinyl-flavin adduct during the photocycle marked with a gray star and ( of e-value) that motifs 1 and 2 are present in a given domain shows clear discrimination between known LOV sensors and closely related protein classes of non-LOV PAS proteins, BLUF domains, and other flavoproteins.When searching for the motifs in known test set LOV domains that were also in the training set, we applied a leave-one-out cross-validation scheme, in which the two sensor motifs were regenerated for the training LOV dataset minus one LOV photoreceptor, and the sensor motifs were then searched for with the MAST tool on the remaining LOV photoreceptor.

These rare functions were found in recently sequenced dikarya, heterokonts, and species diverging early in the evolutionary lineage of green algae, highlighting the importance of sequencing diverse organisms to capture the functional space of photosensory proteins.

This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics.

The light–oxygen–voltage sensitive (LOV) domain subset of the Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim (PAS) superfamily is a ubiquitous photoreceptor class that enables organisms across multiple kingdoms to sense blue light (1–5).

This comprehensive discovery, analysis, and cataloging of LOV domain diversity will inform how light regulates organismal behavior, beget new optogenetic tools or protein-based photocatalysts, and create a foundation for uncovering new insights into LOV photoreceptor structure–function and rational engineering principles through comparative structural genomics. 1) identifies LOV domains by calculating a match score for candidate sequences to custom-developed LOV flavin-binding motifs, represented by position-weighted matrices that ascribe weights to various positions within a sequence pattern according to how strongly those positions are conserved.

Because isolating motifs that relate to flavin binding and photocycling de-emphasizes the highly variable sequence contributions of the effectors also found within the ORF, a motif-based search created a clear stringency cutoff for defining the obligate LOV sensor domain.

The MEME training dataset proteins were selected to span a range of physiological functions, organisms of origin, and ecological niches and have been previously validated to photocycle.

Training and test sets are provided in Dataset S1.) Sequence logos for motifs 1 and 2, identified by the MEME tool for a training set of 18 LOV proteins validated to photocycle, with the cysteine that forms the cysteinyl-flavin adduct during the photocycle marked with a gray star and ( of e-value) that motifs 1 and 2 are present in a given domain shows clear discrimination between known LOV sensors and closely related protein classes of non-LOV PAS proteins, BLUF domains, and other flavoproteins.

Conserved motifs were identified using the Multiple Em for Motif Elicitation (MEME) tool (20), based on 18 well-characterized LOV proteins that were selected to reflect a breadth in structural and functional diversity among known sensors (Fig. Several submotifs had particularly high information contents, including a GX(N/D)C(R/H)(F/I)L(Q/A) submotif containing the key cysteine that forms the cysteinyl-flavin adduct during the LOV photocycle.

Additionally, mutations to conserved residues in FXXXT(G/E)Y and N(Y/F)XXX(G/D)XX(F/L)XN submotifs are also known to impair blue-light sensation (30).

Their modular design is advantageous for engineering chimeras between LOV sensors with effectors of choice, enabling strategies for dynamic gain-of-function of arbitrary proteins in cells.

Thus, elucidating the diversity in the repertoire of effector functions, as well as the diversity in multidomain structural arrangements of LOV sensors and effectors, will respectively deepen collective understanding of what cellular adaptation processes are dynamically regulated by light and how these highly varied signals are transduced by the modular protein architecture in response to a common blue-light stimulus.

More broadly, because PAS proteins share conserved signal transmission mechanisms in response to various sensory inputs (17) that include light (e.g., LOV, phytochrome), ligands (e.g., Cache domains, PDC domains) (18), and oxygen (e.g., HIF proteins) (19), new insights into LOV structure–function will enhance the overall understanding of the PAS superfamily of sensory proteins.

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