A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.

Abstract:

:Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Hasegawa M,Hosaka T,Kojima K,Nishimura Y,Nakajima Y,Kimura-Someya T,Shirouzu M,Sudo Y,Yoshizawa S

doi

10.1038/s41598-020-73606-y

subject

Has Abstract

pub_date

2020-10-07 00:00:00

pages

16752

issue

1

issn

2045-2322

pii

10.1038/s41598-020-73606-y

journal_volume

10

pub_type

杂志文章
  • Long Sleep Duration and Risk of Ischemic Stroke and Hemorrhagic Stroke: the Kailuan Prospective Study.

    abstract::The objective of this study was to examine the relationship between sleep duration and ischemic and hemorrhagic stroke in a community-based cohort. The current analysis included 95,023 Chinese participants who were free of stroke at the baseline survey (2006-2007). Cox proportional hazards models were used to calculat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep33664

    authors: Song Q,Liu X,Zhou W,Wang L,Zheng X,Wang X,Wu S

    更新日期:2016-09-16 00:00:00

  • Responses of crop yield growth to global temperature and socioeconomic changes.

    abstract::Although biophysical yield responses to local warming have been studied, we know little about how crop yield growth-a function of climate and technology-responds to global temperature and socioeconomic changes. Here, we present the yield growth of major crops under warming conditions from preindustrial levels as simul...

    journal_title:Scientific reports

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41598-017-08214-4

    authors: Iizumi T,Furuya J,Shen Z,Kim W,Okada M,Fujimori S,Hasegawa T,Nishimori M

    更新日期:2017-08-10 00:00:00

  • Enhancing elevated temperature strength of copper containing aluminium alloys by forming L12 Al3Zr precipitates and nucleating θ″ precipitates on them.

    abstract::Strengthening by precipitation of second phase is the guiding principle for the development of a host of high strength structural alloys, in particular, aluminium alloys for transportation sector. Higher efficiency and lower emission demands use of alloys at higher operating temperatures (200 °C-250 °C) and stresses, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-11540-2

    authors: Kumar Makineni S,Sugathan S,Meher S,Banerjee R,Bhattacharya S,Kumar S,Chattopadhyay K

    更新日期:2017-09-11 00:00:00

  • Uncovering representations of sleep-associated hippocampal ensemble spike activity.

    abstract::Pyramidal neurons in the rodent hippocampus exhibit spatial tuning during spatial navigation, and they are reactivated in specific temporal order during sharp-wave ripples observed in quiet wakefulness or slow wave sleep. However, analyzing representations of sleep-associated hippocampal ensemble spike activity remain...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep32193

    authors: Chen Z,Grosmark AD,Penagos H,Wilson MA

    更新日期:2016-08-30 00:00:00

  • Stable N-doped & FeNi-decorated graphene non-precious electrocatalyst for Oxygen Reduction Reaction in Acid Medium.

    abstract::NiFe nanoparticles-decorated & N-doped graphene is introduced as an effective and stable non-precious electrocatalyst for ORR in the acid medium. Compared to conventional Pt/C electrodes under the same conditions, the proposed nanocatalyst shows closer onset potential and current density. Typically, the observed onset...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-22114-1

    authors: Barakat NAM,El-Deen AG,Ghouri ZK,Al-Meer S

    更新日期:2018-02-28 00:00:00

  • Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells.

    abstract::Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep19627

    authors: Stingaciu LR,O'Neill H,Liberton M,Urban VS,Pakrasi HB,Ohl M

    更新日期:2016-01-21 00:00:00

  • Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking.

    abstract::Astragalus membranaceus (HUANG QI, HQ) is a kind of traditional Chinese medicine. Researchers have widely concerned its antitumor effect. At present, there is still a lack of research on the treatment of laryngeal cancer with HQ. In this study, we integrated data from the weighted gene co-expression network of larynge...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68093-0

    authors: Dong KF,Huo MQ,Sun HY,Li TK,Li D

    更新日期:2020-07-07 00:00:00

  • Efficacy of Losartan in the management of Post-Dialysis Euvolemic Hypertension (HELD-Trial): A Single-Blind Randomized Control Trial.

    abstract::To assess the effectiveness of losartan 50 mg on post dialysis euvolemic hypertensive patients against standard antihypertensive pharmacotherapy. A multicentre, prospective, randomized, single-blind trial was conducted to assess the effect of losartan 50 mg every other day (EOD), once a morning (OM) among post-dialysi...

    journal_title:Scientific reports

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1038/srep36592

    authors: Aftab RA,Khan AH,Adnan AS,Sulaiman SAS,Khan TM

    更新日期:2016-12-06 00:00:00

  • Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia.

    abstract::The semantic variant of primary progressive aphasia (svPPA) is a clinical syndrome characterized by neurodegeneration and progressive loss of semantic knowledge. Unlike many other forms of frontotemporal lobar degeneration (FTLD), svPPA has a highly consistent underlying pathology composed of TDP-43 (a regulator of RN...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-46415-1

    authors: Bonham LW,Steele NZR,Karch CM,Broce I,Geier EG,Wen NL,Momeni P,Hardy J,Miller ZA,Gorno-Tempini ML,Hess CP,Lewis P,Miller BL,Seeley WW,Manzoni C,Desikan RS,Baranzini SE,Ferrari R,Yokoyama JS,International FTD-Genomic

    更新日期:2019-07-26 00:00:00

  • Obesity, adipokines, and C-peptide are associated with distinct plasma phospholipid profiles in adult males, an untargeted lipidomic approach.

    abstract::Obesity is associated with dysregulated lipid metabolism and adipokine secretion. Our group has previously reported obesity and adipokines are associated with % total fatty acid (FA) differences in plasma phospholipids. The objective of our current study was to identify in which complex lipid species (i.e., phosphatid...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05785-0

    authors: Pickens CA,Vazquez AI,Jones AD,Fenton JI

    更新日期:2017-07-24 00:00:00

  • Genetic diversity of the intimin gene (eae) in non-O157 Shiga toxin-producing Escherichia coli strains in China.

    abstract::Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. The increasing incidence of non-O157 STEC has posed a great risk to public health. Besides the Shiga toxin (Stx), the adherence factor, intimin, coded by eae gene plays a critical role in STEC pathogenesis. In this study, we investigated...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60225-w

    authors: Yang X,Sun H,Fan R,Fu S,Zhang J,Matussek A,Xiong Y,Bai X

    更新日期:2020-02-24 00:00:00

  • Transcriptome analysis of genes involved in secondary cell wall biosynthesis in developing internodes of Miscanthus lutarioriparius.

    abstract::Miscanthus is a promising lignocellulosic bioenergy crop for bioethanol production. To identify candidate genes and regulation networks involved in secondary cell wall (SCW) development in Miscanthus, we performed de novo transcriptome analysis of a developing internode. According to the histological and in-situ histo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08690-8

    authors: Hu R,Xu Y,Yu C,He K,Tang Q,Jia C,He G,Wang X,Kong Y,Zhou G

    更新日期:2017-08-22 00:00:00

  • Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing.

    abstract::Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15076-3

    authors: Pradhan B,Cajuso T,Katainen R,Sulo P,Tanskanen T,Kilpivaara O,Pitkänen E,Aaltonen LA,Kauppi L,Palin K

    更新日期:2017-11-06 00:00:00

  • The NMDA receptor GluN2C subunit controls cortical excitatory-inhibitory balance, neuronal oscillations and cognitive function.

    abstract::Despite strong evidence for NMDA receptor (NMDAR) hypofunction as an underlying factor for cognitive disorders, the precise roles of various NMDAR subtypes remains unknown. The GluN2C-containing NMDARs exhibit unique biophysical properties and expression pattern, and lower expression of GluN2C subunit has been reporte...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38321

    authors: Gupta SC,Ravikrishnan A,Liu J,Mao Z,Pavuluri R,Hillman BG,Gandhi PJ,Stairs DJ,Li M,Ugale RR,Monaghan DT,Dravid SM

    更新日期:2016-12-06 00:00:00

  • p66Shc: A novel biomarker of tubular oxidative injury in patients with diabetic nephropathy.

    abstract::Increased p66Shc expression has been associated with diabetic nephropathy (DN). However, whether p66Shc can serve as a potential biomarker for tubular oxidative injury in DN is unknown. We measured the expression of p66Shc in peripheral blood monocytes (PBMs) and renal biopsy tissues from DN patients and then analysed...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29302

    authors: Xu X,Zhu X,Ma M,Han Y,Hu C,Yuan S,Yang Y,Xiao L,Liu F,Kanwar YS,Sun L

    更新日期:2016-07-05 00:00:00

  • VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis.

    abstract::Untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. Conjugative DNA transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep24643

    authors: Fercher C,Probst I,Kohler V,Goessweiner-Mohr N,Arends K,Grohmann E,Zangger K,Meyer NH,Keller W

    更新日期:2016-04-22 00:00:00

  • Variation in leaf morphological, stomatal, and anatomical traits and their relationships in temperate and subtropical forests.

    abstract::Leaf functional traits have attracted the attention of ecologists for several decades, but few studies have systematically assessed leaf morphological traits (termed "economic traits"), stomatal (termed "hydraulic"), and anatomical traits of entire forest communities, thus it is unclear whether their relationships are...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42335-2

    authors: Liu C,Li Y,Xu L,Chen Z,He N

    更新日期:2019-04-09 00:00:00

  • Garnet, the archetypal cubic mineral, grows tetragonal.

    abstract::Garnet is the archetypal cubic mineral, occurring in a wide variety of rock types in Earth's crust and upper mantle. Owing to its prevalence, durability and compositional diversity, garnet is used to investigate a broad range of geological processes. Although birefringence is a characteristic feature of rare Ca-Fe3+ g...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-51214-9

    authors: Cesare B,Nestola F,Johnson T,Mugnaioli E,Della Ventura G,Peruzzo L,Bartoli O,Viti C,Erickson T

    更新日期:2019-10-11 00:00:00

  • Circulating proteomic signature for detection of biomarkers in bladder cancer patients.

    abstract::The identification of clinically-relevant early diagnostic and prognostic protein biomarkers is essential to maximize therapeutic efficacy and prevent cancer progression. The aim of the current study is to determine whether aberrant plasma protein profile can be applied as a surrogate tool for early diagnosis of bladd...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67929-z

    authors: Nedjadi T,Benabdelkamal H,Albarakati N,Masood A,Al-Sayyad A,Alfadda AA,Alanazi IO,Al-Ammari A,Al-Maghrabi J

    更新日期:2020-07-03 00:00:00

  • Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis.

    abstract::The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system's components. Translation initiation in mitochondria is assisted by two general initiation ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep18749

    authors: Kuzmenko A,Derbikova K,Salvatori R,Tankov S,Atkinson GC,Tenson T,Ott M,Kamenski P,Hauryliuk V

    更新日期:2016-01-05 00:00:00

  • Diabetes Stimulates Osteoclastogenesis by Acidosis-Induced Activation of Transient Receptor Potential Cation Channels.

    abstract::Patients with type 1 diabetes have lower bone mineral density and higher risk of fractures. The role of osteoblasts in diabetes-related osteoporosis is well acknowledged whereas the role of osteoclasts (OCLs) is still unclear. We hypothesize that OCLs participate in pathological bone remodeling. We conducted studies i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30639

    authors: Reni C,Mangialardi G,Meloni M,Madeddu P

    更新日期:2016-07-29 00:00:00

  • Immune Response of A Novel ATR-AP205-001 Conjugate Anti-hypertensive Vaccine.

    abstract::We developed a virus-like particle (VLP)-based therapeutic vaccine against angiotensin II receptor type 1, ATR-AP205-001, which could significantly reduce the blood pressure and protect target organs of hypertensive animals. In this study, we focused on the immunological effect and safety of the VLP-based vaccine. By ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-12996-y

    authors: Hu X,Deng Y,Chen X,Zhou Y,Zhang H,Wu H,Yang S,Chen F,Zhou Z,Wang M,Qiu Z,Liao Y

    更新日期:2017-10-03 00:00:00

  • Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders.

    abstract::In a previous study, we proposed that age-related mitochondrial respiration defects observed in elderly subjects are partially due to age-associated downregulation of nuclear-encoded genes, including serine hydroxymethyltransferase 2 (SHMT2), which is involved in mitochondrial one-carbon (1C) metabolism. This assertio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52372-6

    authors: Tani H,Mito T,Velagapudi V,Ishikawa K,Umehara M,Nakada K,Suomalainen A,Hayashi JI

    更新日期:2019-11-05 00:00:00

  • Tunable graphene-based mid-infrared plasmonic wide-angle narrowband perfect absorber.

    abstract::In this paper, the periodic double-layer graphene ribbon arrays placed near a metallic ground plate coated by a dielectric layer are proposed and analyzed by the coupled-mode theory (CMT) to predict the perfect absorption response in the mid-infrared region. Numerical simulations of the finite-difference time-domain (...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36651

    authors: Li H,Wang L,Zhai X

    更新日期:2016-11-15 00:00:00

  • Advanced Raman Spectroscopy of Methylammonium Lead Iodide: Development of a Non-destructive Characterisation Methodology.

    abstract::In recent years, there has been an impressively fast technological progress in the development of highly efficient lead halide perovskite solar cells. However, the stability of perovskite films and respective solar cells is still an open point of concern and calls for advanced characterization methods. In this work, w...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep35973

    authors: Pistor P,Ruiz A,Cabot A,Izquierdo-Roca V

    更新日期:2016-10-27 00:00:00

  • Air-mode photonic crystal ring resonator on silicon-on-insulator.

    abstract::In this report, we propose and demonstrate an air-mode photonic crystal ring resonator (PhCRR) on silicon-on-insulator platform. Air mode is utilized to confine the optical field into photonic crystal (PhC) air holes, which is confirmed by the three-dimensional finite-difference time-domain simulation. PhCRR structure...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep19999

    authors: Gao G,Zhang Y,Zhang H,Wang Y,Huang Q,Xia J

    更新日期:2016-01-28 00:00:00

  • A novel signature for stratifying the molecular heterogeneity of the tissue-infiltrating T-cell receptor repertoire reflects gastric cancer prognosis.

    abstract::Many basic properties of the T-cell receptor (TCR) repertoire require clarification, and the changes occurring in the TCR repertoire during carcinogenesis, especially during precancerous stages, remain unclear. This study used deep sequencing analyses to examine 41 gastric tissue samples at different pathological stag...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08289-z

    authors: Kuang M,Cheng J,Zhang C,Feng L,Xu X,Zhang Y,Zu M,Cui J,Yu H,Zhang K,Yang A,Cheng S

    更新日期:2017-08-10 00:00:00

  • Limiting the Spectral Diffusion of Nano-Scale Light Emitters using the Purcell effect in a Photonic-Confined Environment.

    abstract::Partial suppression of the spectral diffusion of quantum dot (QD) excitons tuned to resonance of a nano-photonic cavity is reported. The suppression is caused by the Purcell enhancement of the QD-exciton recombination rate, which alters the rate of charging of the solid-state environment by the QD itself. The effect c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37677-2

    authors: Lyasota A,Jarlov C,Rudra A,Dwir B,Kapon E

    更新日期:2019-02-04 00:00:00

  • A virtual experimenter does not increase placebo hypoalgesia when delivering an interactive expectancy manipulation.

    abstract::Lack of standardization and unblinding threaten the research of mechanisms involved in expectancy effects on pain. We evaluated a computer-controlled virtual experimenter (VEx) to avoid these issues. Fifty-four subjects underwent a baseline-retest heat pain protocol. Between sessions, they received an expectancy manip...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77453-9

    authors: Horing B,Beadle SC,Inks Z,Robb A,Muth ER,Babu SV

    更新日期:2020-11-23 00:00:00

  • Reciprocal regulation of RORγt acetylation and function by p300 and HDAC1.

    abstract::T helper 17 (Th17) cells not only play critical roles in protecting against bacterial and fungal infections but are also involved in the pathogenesis of autoimmune diseases. The retinoic acid-related orphan receptor (RORγt) is a key transcription factor involved in Th17 cell differentiation through direct transcriptio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep16355

    authors: Wu Q,Nie J,Gao Y,Xu P,Sun Q,Yang J,Han L,Chen Z,Wang X,Lv L,Tsun A,Shen J,Li B

    更新日期:2015-11-09 00:00:00