Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins

Nakajima, Yu; Kojima, Keiichi; Kashiyama, Yuichiro; Doi, Satoko; Nakai, Ryosuke; Sudo, Yuki; Kogure, Kazuhiro; Yoshizawa, Susumu

doi:10.1264/jsme2.me20085

Cited by 18 publications

(12 citation statements)

References 38 publications

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“…However, it has been demonstrated that rhodopsin-based phototrophy can also be carried out in hypoxic and anoxic conditions ( DasSarma et al 2012 ). In addition, an alternative, uncharacterized biosynthetic pathway for retinal synthesis has been reported ( Nakajima et al 2020 ; Chazan et al 2022 ). Thus, the necessity of oxygen for retinal synthesis remains an open question.…”

Section: Resultsmentioning

confidence: 99%

Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins

Sephus

Fer

Garcia

et al. 2022

Molecular Biology and Evolution

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For billions of years, life has continuously adapted to dynamic physical conditions near the Earth’s surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth’s earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as “paleosensors” for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.

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Section: Resultsmentioning

confidence: 99%

Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins

Sephus

Fer

Garcia

et al. 2022

Molecular Biology and Evolution

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“…However, in all members of the LGC subclade, the gene coding for isopentenyl diphosphate isomerase ( isp A) is not present. This genomic deletion forces the bacterium to retrieve retinal from the environment, like many other marine streamlined organisms ( 46 , 61 , 62 ). Despite the different evolutionary trajectories in terms of genomic architecture, at the functional level, the two subclades appear to have many similarities including the absence of essential genes in certain pathways, suggesting that multiple traits have been conserved through vertical inheritance.…”

Section: Resultsmentioning

confidence: 99%

Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle

et al. 2021

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The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes.

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“…However, recent analysis of A. minutum KCN T found that this strain synthesizes retinal via a still-unknown pathway [51], which could be shared with strain MWH-Mo1 T . It is possible that retinal is produced by MWH-Mo1 T by this uncharacterized pathway under conditions that have not yet been identified.…”

Section: Ecologymentioning

confidence: 99%

Aurantimicrobium photophilum sp. nov., a non-photosynthetic bacterium adjusting its metabolism to the diurnal light cycle and reclassification of Cryobacterium mesophilum as Terrimesophilobacter mesophilus gen. nov., comb. nov.

Hahn

Pitt

Koll

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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The aerobic primarily chemoorganotrophic actinobacterial strain MWH-Mo1T was isolated from a freshwater lake and is characterized by small cell lengths of less than 1 µm, small cell volumes of 0.05–0.06 µm3 (ultramicrobacterium), a small genome size of 1.75 Mbp and, at least for an actinobacterium, a low DNA G+C content of 54.6 mol%. Phylogenetic analyses based on concatenated amino acid sequences of 116 housekeeping genes suggested the type strain of Aurantimicrobium minutum affiliated with the family Microbacteriaceae as its closest described relative. Strain MWH-Mo1T shares with the type strain of that species a 16S rRNA gene sequence similarity of 99.6 % but the genomes of the two strains share an average nucleotide identity of only 79.3 %. Strain MWH-Mo1T is in many genomic, phenotypic and chemotaxonomic characteristics quite similar to the type strain of A. minutum . Previous intensive investigations revealed two unusual traits of strain MWH-Mo1T. Although the strain is not known to be phototrophic, the metabolism is adjusted to the diurnal light cycle by up- and down-regulation of genes in light and darkness. This results in faster growth in the presence of light. Additionally, a cell size-independent protection against predation by bacterivorous flagellates, most likely mediated by a proteinaceous cell surface structure, was demonstrated. For the previously intensively investigated aerobic chemoorganotrophic actinobacterial strain MWH-Mo1T (=CCUG 56426T=DSM 107758T), the establishment of the new species Aurantimicrobium photophilum sp. nov. is proposed.

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Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins

Cited by 18 publications

References 38 publications

Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins

Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins

Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle

Aurantimicrobium photophilum sp. nov., a non-photosynthetic bacterium adjusting its metabolism to the diurnal light cycle and reclassification of Cryobacterium mesophilum as Terrimesophilobacter mesophilus gen. nov., comb. nov.

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