In the vast expanses of the world’s oceans, microscopic life forms have evolved intricate mechanisms to harness sunlight and sustain marine ecosystems. Among these, microbial rhodopsins stand out as pivotal photoreceptor proteins that convert light energy into biochemical signals or ion gradients, directly supporting marine microbial life. Traditionally, microbial rhodopsins rely on retinal, a derivative of vitamin A, as their sole chromophore—the light-absorbing molecule that initiates their photochemical activity. However, recent discoveries are challenging this long-held notion, revealing that in certain marine bacteria, additional pigments called carotenoids not only bind to rhodopsins but crucially enhance their light-harvesting capabilities.
A groundbreaking study led by Fujiwara et al. (2025) has illuminated the complex interplay between carotenoids and rhodopsins in the marine bacterial phylum Bacteroidota, specifically focusing on the isolate Nonlabens marinus S1-08^T. These bacteria inhabit the sunlit surface waters, relying heavily on efficient light utilization to thrive in nutrient-variable oceans. The research unveils how carotenoids, traditionally understood as light-protective pigments and antioxidants, serve an active role as antenna molecules. By attaching to rhodopsins, they facilitate energy transfer to retinal, thereby broadening the spectral range of light these proteins can exploit. This finding not only revises our understanding of rhodopsin photoreception but also has profound implications for modeling marine microbial photobiology.
At the core of this discovery is the demonstration that the carotenoid myxol forms stable complexes with two distinct types of rhodopsins found in Nonlabens marinus: proteorhodopsin and a chloride ion-pumping rhodopsin. Proteorhodopsin has garnered considerable attention in marine microbiology as a widespread proton pump capable of harnessing green light, aiding in ATP synthesis, and contributing to cellular energy budgets. The newly studied chloride-pumping rhodopsin adds a layer of functional diversity, managing ion transport crucial for cellular homeostasis. Both rhodopsins, when bound to myxol, exhibited enhanced photochemical properties, with energy transfer from carotenoid to retinal confirmed through sensitive spectroscopic analyses.
Functional assays conducted by the researchers revealed that carotenoid binding significantly accelerates the photocycle dynamics of these rhodopsins. The photocycle—the sequence of conformational and chemical changes rhodopsins undergo upon photon absorption—dictates how efficiently light energy is converted to molecular work. An accelerated photocycle means that the rhodopsins can process photons more rapidly, effectively increasing the rate of energy conversion. This enhancement boosts the light utilization efficiency of proteorhodopsin, enabling the bacteria to make better use of dim or variable light conditions prevalent in many ocean surface layers. Such efficiency gains could provide a competitive edge in microbial niches where light and nutrients are limiting.
The researchers employed cryogenic electron microscopy (cryo-EM) to unravel the molecular architecture of these carotenoid–rhodopsin assemblies. The high-resolution structures revealed intimate binding sites where myxol nestles alongside retinal within the rhodopsin protein framework. This spatial proximity facilitates efficient Förster resonance energy transfer (FRET) from the carotenoid’s excited state to retinal’s chromophore. The structural data provide crucial insights into how carotenoid binding does not merely protect rhodopsins from photodamage—as previously suspected—but plays an active mechanistic role in enhancing photoreceptor performance.
These findings gain further significance considering the ecological prevalence of Bacteroidota rhodopsins. Metatranscriptomic analyses performed across diverse marine photic zone samples indicate that this phylum’s rhodopsins are widely expressed and likely contribute substantially to the ocean’s primary bioenergetic processes. The conservation of carotenoid-binding motifs in these proteins suggests that the evolutionary integration of carotenoid antennas is a common strategy among marine Bacteroidota to optimize light harvesting. This adaptation may be particularly advantageous in fluctuating irradiance environments such as coastal waters and open ocean surface layers where light spectra and intensities vary dynamically.
Beyond its ecological implications, this study also bridges a gap in understanding the functional diversity of microbial rhodopsins. Unlike animal rhodopsins, whose light-absorbing chromophore has been well-established, the role of accessory pigments in microbial rhodopsins was largely speculative. The revelation that carotenoids act as photocycle-accelerating pigments opens new avenues for exploring light-driven energy transduction in microorganisms and may inspire bioengineering approaches to designing novel light-harvesting systems.
Moreover, the multifunctionality of carotenoids, historically studied for their antioxidative properties in photosynthetic organisms, is expanded in this marine microbial context. The dual role of carotenoids as both photoprotectants and active participants in light capture hints at evolutionary pressures that have shaped microbial photoreceptors to maximize efficiency. Such complexity highlights the intricate interactions between microbial proteins and pigments, pushing the boundaries of current biophotonic paradigms.
In terms of biochemical implications, the study enriches our understanding of proton-pumping dynamics in proteorhodopsins. The acceleration of the photocycle by carotenoid binding potentially improves proton flux across bacterial membranes, increasing the generation of proton motive force and ultimately cellular ATP production. Similarly, the facilitated function of chloride ion-pumping rhodopsins through carotenoid interaction may affect ion homeostasis, contributing to cell survival under varying salinity conditions. These integrated light and ion transport mechanisms underscore the sophisticated energy management strategies bacteria employ in ocean environments.
The methodological approach combining microbiological isolation, pigment reconstitution, spectroscopy, and cryo-EM is noteworthy. By working with native pigments and proteins from environmental isolates rather than heterologous expression systems alone, the study ensures physiological relevance and authenticity in the observed interactions. The multi-disciplinary nature of the research, integrating structural biology with marine microbiology and photophysics, exemplifies cutting-edge science poised to redefine our understanding of microbial ecology.
Looking ahead, the elucidation of carotenoid–rhodopsin complexes could inspire exploration of similar pigment-protein interactions in other marine microbes. If carotenoids prove to be widespread accessory light harvesters, their presence would warrant reassessment of marine light utilization models and biogeochemical cycling predictions. Furthermore, insights into energy transfer mechanisms might translate into innovations in synthetic biology, where engineered light-harvesting systems could enhance bioenergetic efficiencies in microbial cell factories or solar energy applications.
In conclusion, this landmark study by Fujiwara et al. represents a paradigm shift in our appreciation of how marine bacteria capture and convert sunlight. By demonstrating that carotenoids directly bind to and modulate rhodopsins, acting as photocycle-accelerating pigments, the work uncovers a new layer of complexity in microbial photobiology. These discoveries not only advance fundamental biology but also prompt reevaluation of marine microbial roles in oceanic phototrophic energy dynamics, with potential ripple effects across ecology, biotechnology, and climate science.
Subject of Research: The study investigates the interaction between carotenoids and rhodopsins in marine Bacteroidota bacteria, revealing how carotenoid binding enhances photochemical activity and accelerates the photocycle of microbial rhodopsins.
Article Title: Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota
Article References:
Fujiwara, T., Hosaka, T., Hasegawa-Takano, M. et al. Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.
Nat Microbiol (2025). https://doi.org/10.1038/s41564-025-02109-1
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