Dohmen, R. | Search bioRxiv

bioRxiv2025

Functional insights into the photoactive yellow protein family from homologs, multidomain proteins and inferred pyp operons

Photoactive Yellow Protein (PYP) is a model system for functional protein dynamics and a prototype of the PAS domain superfamily. It is a bacterial photoreceptor that triggers a range of responses in different bacteria: phototaxis, biosynthesis of photo-protective pigments, and light regulation of biofilm formation. An important gap in knowledge on PYP is the signal transduction chain that guides the initial signal from the photoreceptor to various biological responses. Here we report an expanded set of 984 PYP homologs, providing information on sequence conservation and variation. We analyze this set of PYPs using two bioinformatics approaches to identify candidate proteins that are functionally related to PYP. First, we identified 153 multi-domain proteins containing PYP and analyzed the domain composition of these proteins. Specific preferences for N- or C-terminal placement of the PYP domain were observed. Second, we identified 113 predicted multi-gene operons containing the pyp gene. These two approaches yielded multiple candidates for proteins in the signal transduction chain associated with PYP, particularly histidine kinase (implying phosphorylation), methyl accepting chemotaxis protein (implying phototaxis), and GGDEF and EAL proteins (implying a role of c-di-GMP and biofilm formation). Some of these candidates were present only in multi-domain proteins and others only in pyp operons. Overexpression of the PYP domain from the MCP-fusion protein from Nitrincola alkalilacustris yielded a protein with an absorbance maximum of 447 nm and an overall photocycle rate of 0.5 seconds. Our results provide a clear basis for future experimental work on identifying signal transduction partners of PYP.

microbiology↗

bioRxiv2021

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth. ImportanceThe Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcoat are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota has been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remains unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity we confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate rductio, and dissimilarity sulfate reduction for energy acquisition. Our result highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcoat has occurred in response to soil formation as a distinct habitat on earth.

microbiology↗