1
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Villanueva CD, Bohunická M, Johansen JR. We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy. JOURNAL OF PHYCOLOGY 2024. [PMID: 39152777 DOI: 10.1111/jpy.13491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/19/2024]
Abstract
The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes.
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Affiliation(s)
- Chelsea D Villanueva
- Department of Biological, Geological, & Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
- Department of Biology, John Carroll University, University Heights, Ohio, USA
| | - Markéta Bohunická
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, USA
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2
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Xu HF, Yu C, Bai Y, Zuo AW, Ye YT, Liu YR, Li ZK, Dai GZ, Chen M, Qiu BS. Red-light-dependent chlorophyll synthesis kindles photosynthetic recovery of chlorotic dormant cyanobacteria using a dark-operative enzyme. Curr Biol 2024:S0960-9822(24)01022-4. [PMID: 39146941 DOI: 10.1016/j.cub.2024.07.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Chlorosis dormancy resulting from nitrogen starvation and its resuscitation upon available nitrogen contributes greatly to the fitness of cyanobacterial population under nitrogen-fluctuating environments. The reinstallation of the photosynthetic machinery is a key process for resuscitation from a chlorotic dormant state; however, the underlying regulatory mechanism is still elusive. Here, we reported that red light is essential for re-greening chlorotic Synechocystis sp. PCC 6803 (a non-diazotrophic cyanobacterium) after nitrogen supplement under weak light conditions. The expression of dark-operative protochlorophyllide reductase (DPOR) governed by the transcriptional factor RpaB was strikingly induced by red light in chlorotic cells, and its deficient mutant lost the capability of resuscitation from a dormant state, indicating DPOR catalyzing chlorophyll synthesis is a key step in the photosynthetic recovery of dormant cyanobacteria. Although light-dependent protochlorophyllide reductase is widely considered as a master switch in photomorphogenesis, this study unravels the primitive DPOR as a spark to activate the photosynthetic recovery of chlorotic dormant cyanobacteria. These findings provide new insight into the biological significance of DPOR in cyanobacteria and even some plants thriving in extreme environments.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Chen Yu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Yang Bai
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Ai-Wei Zuo
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Ying-Tong Ye
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Yan-Ru Liu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Zheng-Ke Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Guo-Zheng Dai
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Min Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Bao-Sheng Qiu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China.
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3
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Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. JOURNAL OF PHYCOLOGY 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
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Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
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4
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Yang YW, Liu K, Huang D, Yu C, Chen SZ, Chen M, Qiu BS. Functional specialization of expanded orange carotenoid protein paralogs in subaerial Nostoc species. PLANT PHYSIOLOGY 2023:kiad234. [PMID: 37070859 DOI: 10.1093/plphys/kiad234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Orange carotenoid protein (OCP) is a photoactive protein that participates in the photoprotection of cyanobacteria. There are two full-length OCP proteins, four N-terminal paralogs (helical carotenoid protein, HCP), and one C-terminal domain-like carotenoid protein (CCP) found in Nostoc flagelliforme, a desert cyanobacterium. All HCPs (HCP1-3 and HCP6) from N. flagelliforme demonstrated their excellent singlet oxygen quenching activities, in which HCP2 was the strongest singlet oxygen quencher compared with others. Two OCPs, OCPx1 and OCPx2, were not involved in singlet oxygen scavenging; instead, they functioned as phycobilisome fluorescence quenchers. The fast-acting OCPx1 showed more effective photoactivation and stronger phycobilisome fluorescence quenching compared to OCPx2, which behaved differently from all reported OCP paralogs. The resolved crystal structure and mutant analysis revealed that Trp111 and Met125 play essential roles in OCPx2, which is dominant and long-acting. The resolved crystal structure of OCPx2 is maintained in a monomer state and showed more flexible regulation in energy quenching activities compared with the packed oligomer of OCPx1. The recombinant apo-CCP obtained the carotenoid pigment from holo-HCPs and holo-OCPx1 of N. flagelliforme. No such carotenoid transferring processes were observed between apo-CCP and holo-OCPx2. The close phylogenetic relationship of OCP paralogs from subaerial Nostoc species indicates an adaptive evolution toward development of photoprotection: protecting cellular metabolism against singlet oxygen damage using HCPs and against excess energy captured by active phycobilisomes using two different working modes of OCPx.
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Affiliation(s)
- Yi-Wen Yang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
- College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, Jiangxi 332000, China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
| | - Da Huang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
| | - Chen Yu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
| | - Si-Zhuo Chen
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
| | - Min Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, China
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5
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Pakharukova MY, Lishai EA, Zaparina O, Baginskaya NV, Hong SJ, Sripa B, Mordvinov VA. Opisthorchis viverrini, Clonorchis sinensis and Opisthorchis felineus liver flukes affect mammalian host microbiome in a species-specific manner. PLoS Negl Trop Dis 2023; 17:e0011111. [PMID: 36780567 PMCID: PMC9956601 DOI: 10.1371/journal.pntd.0011111] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/24/2023] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Opisthorchis felineus, Opisthorchis viverrini and Clonorchis sinensis are epidemiologically significant food-borne trematodes endemic to diverse climatic areas. O. viverrini and C. sinensis are both recognized to be 1A group of biological carcinogens to human, whereas O. felineus is not. The mechanisms of carcinogenesis by the liver flukes are studied fragmentarily, the role of host and parasite microbiome is an unexplored aspect. METHODOLOGY/PRINCIPAL FINDINGS Specific pathogen free Mesocricetus auratus hamsters were infected with C. sinensis, O. viverrini and O. felineus. The microbiota of the adult worms, colon feces and bile from the hamsters was investigated using Illumina-based sequencing targeting the prokaryotic 16S rRNA gene. The analysis of 43 libraries revealed 18,830,015 sequences, the bacterial super-kingdom, 16 different phyla, 39 classes, 63 orders, 107 families, 187 genera-level phylotypes. O. viverrini, a fluke with the most pronounced carcinogenic potential, has the strongest impact on the host bile microbiome, changing the abundance of 92 features, including Bifidobacteriaceae, Erysipelotrichaceae, [Paraprevotellaceae], Acetobacteraceae, Coriobacteraceae and Corynebacteriaceae bacterial species. All three infections significantly increased Enterobacteriaceae abundance in host bile, reduced the level of commensal bacteria in the gut microbiome (Parabacteroides, Roseburia, and AF12). CONCLUSIONS/SIGNIFICANCE O. felineus, O. viverrini, and C. sinensis infections cause both general and species-specific qualitative and quantitative changes in the composition of microbiota of bile and colon feces of experimental animals infected with these trematodes. The alterations primarily concern the abundance of individual features and the phylogenetic diversity of microbiomes of infected hamsters.
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Affiliation(s)
- Maria Y. Pakharukova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Ekaterina A. Lishai
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Oxana Zaparina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nina V. Baginskaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Sung-Jong Hong
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon, Korea
| | - Banchob Sripa
- WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Center, Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Viatcheslav A. Mordvinov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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6
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Kimura S, Sato M, Fan X, Ohmori M, Ehira S. The two-component response regulator OrrA confers dehydration tolerance by regulating avaKa expression in the cyanobacterium Anabaena sp. strain PCC 7120. Environ Microbiol 2022; 24:5165-5173. [PMID: 36054741 PMCID: PMC9804601 DOI: 10.1111/1462-2920.16162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/06/2022] [Indexed: 01/05/2023]
Abstract
The cyanobacterium Anabaena sp. strain PCC 7120 exhibits dehydration tolerance. The regulation of gene expression in response to dehydration is crucial for the acquisition of dehydration tolerance, but the molecular mechanisms underlying dehydration responses remain unknown. In this study, the functions of the response regulator OrrA in the regulation of salt and dehydration responses were investigated. Disruption of orrA abolished or diminished the induction of hundreds of genes in response to salt stress and dehydration. Thus, OrrA is a principal regulator of both stress responses. In particular, OrrA plays a crucial role in dehydration tolerance because an orrA disruptant completely lost the ability to regrow after dehydration. Moreover, in the OrrA regulon, avaKa encoding a protein of unknown function was revealed to be indispensable for dehydration tolerance. OrrA and AvaK are conserved among the terrestrial cyanobacteria, suggesting their conserved functions in dehydration tolerance in cyanobacteria.
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Affiliation(s)
- Satoshi Kimura
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan
| | - Miho Sato
- Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
| | - Xingyan Fan
- Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
| | - Masayuki Ohmori
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan
| | - Shigeki Ehira
- Department of Biochemistry and Molecular Biology, Faculty of ScienceSaitama UniversitySaitamaJapan,Department of Biological Sciences, Graduate school of ScienceTokyo Metropolitan UniversityTokyoJapan
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7
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Coevolution of tandemly repeated hlips and RpaB-like transcriptional factor confers desiccation tolerance to subaerial Nostoc species. Proc Natl Acad Sci U S A 2022; 119:e2211244119. [PMID: 36215485 PMCID: PMC9586280 DOI: 10.1073/pnas.2211244119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desert-inhabiting cyanobacteria can tolerate extreme desiccation and quickly revive after rehydration. The regulatory mechanisms that enable their vegetative cells to resurrect upon rehydration are poorly understood. In this study, we identified a single gene family of high light-inducible proteins (Hlips) with dramatic expansion in the Nostoc flagelliforme genome and found an intriguingly special convergence formed through four tandem gene duplication. The emerged four independent hlip genes form a gene cluster (hlips-cluster) and respond to dehydration positively. The gene mutants in N. flagelliforme were successfully generated by using gene-editing technology. Phenotypic analysis showed that the desiccation tolerance of hlips-cluster-deleted mutant decreased significantly due to impaired photosystem II repair, whereas heterologous expression of hlips-cluster from N. flagelliforme enhanced desiccation tolerance in Nostoc sp. PCC 7120. Furthermore, a transcription factor Hrf1 (hlips-cluster repressor factor 1) was identified and shown to coordinately regulate the expression of hlips-cluster and desiccation-induced psbAs. Hrf1 acts as a negative regulator for the adaptation of N. flagelliforme to the harsh desert environment. Phylogenetic analysis revealed that most species in the Nostoc genus possess both tandemly repeated Hlips and Hrf1. Our results suggest convergent evolution of desiccation tolerance through the coevolution of tandem Hlips duplication and Hrf1 in subaerial Nostoc species, providing insights into the mechanism of desiccation tolerance in photosynthetic organisms.
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8
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Wang M, Zhu Q, Li X, Hu J, Song F, Liang W, Ma X, Wang L, Liang W. Effect of Drought Stress on Degradation and Remodeling of Membrane Lipids in Nostoc flagelliforme. Foods 2022; 11:foods11121798. [PMID: 35741996 PMCID: PMC9222375 DOI: 10.3390/foods11121798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Nostoc flagelliforme is a kind of terrestrial edible cyanobacteria with important ecological and economic value which has developed special mechanisms to adapt to drought conditions. However, the specific mechanism of lipidome changes in drought tolerance of N. flagelliforme has not been well understood. In this study, the ultra-high-performance liquid chromatography and mass spectrometry were employed to analyze the lipidome changes of N. flagelliforme under dehydration. A total of 853 lipid molecules were identified, of which 171 were significantly different from that of the control group. The digalactosyldiacylglycerol/monogalactosyldiacylglycerol (DGDG/MGDG) ratio was increased. The amount of wax ester (WE) was sharply decreased during drought stress, while Co (Q10) was accumulated. The levels of odd chain fatty acids (OCFAs) were increased under dehydration, positively responding to drought stress according to the energy metabolism state. In conclusion, the lipidomic data corroborated that oxidation, degradation, and biosynthesis of membrane lipids took place during lipid metabolism, which can respond to drought stress through the transformation of energy and substances. Besides, we constructed a lipid metabolic model demonstrating the regulatory mechanism of drought stress in N. flagelliforme. The present study provides insight into the defense strategies of cyanobacteria in lipid metabolic pathways.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wenyu Liang
- Correspondence: ; Tel./Fax: +86-0951-206-2810
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9
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Shen LQ, Zhang ZC, Shang JL, Li ZK, Chen M, Li R, Qiu BS. Kovacikia minuta sp. nov. (Leptolyngbyaceae, Cyanobacteria), a new freshwater chlorophyll f-producing cyanobacterium. JOURNAL OF PHYCOLOGY 2022; 58:424-435. [PMID: 35279831 DOI: 10.1111/jpy.13248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
A few groups of cyanobacteria have been characterized as having far-red light photoacclimation (FaRLiP) that results from chlorophyll f (Chl f) production. In this study, using a polyphasic approach, we taxonomically transferred the Cf. Leptolyngbya sp. CCNUW1 isolated from a shaded freshwater pond, which produces Chl f under far-red light, to the genus Kovacikia and named this taxon Kovacikia minuta sp. nov. This strain was morphologically similar to Leptolyngbya-like strains. The thin filaments were purplish-brown under white light but became grass green under far-red light. The 31-gene phylogeny grouped K. minuta CCNU0001 into order Synechococcales and family Leptolyngbyaceae. Phylogenetic analysis based on 16S rRNA gene sequences further showed that K. minuta CCNU0001 was clustered into Kovacikia with similarities of 97.2-97.4% to the recently reported type species of Kovacikia muscicola HA7619-LM3. Additionally, the internal transcribed spacer region between 16S-23S rRNA genes had a unique sequence and secondary structure compared with other Kovacikia strains and phylogenetically related taxa. Draft genome sequences of K. minuta CCNU0001 (8,564,336 bp) were assembled into one circular chromosome and two circular plasmids. A FaRLiP 20-gene cluster comprised two operons with the unique organization. In sum, K. minuta was established as a new species, and it is the first species reported to produce Chl f and for which a draft genome was produced in genus Kovacikia. This study expanded our knowledge regarding the diversity of Chl f-producing cyanobacteria in far-red light-enriched environments and provides important foundational information for future investigations of FaRLiP evolution in cyanobacteria.
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Affiliation(s)
- Li-Qin Shen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Zhong-Chun Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jin-Long Shang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Zheng-Ke Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Min Chen
- ARC Centre of Excellence for Translational Photosynthesis, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Renhui Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Bao-Sheng Qiu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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10
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Xu HF, Dai GZ, Wang YJ, Cheng C, Shang JL, Li RH, Liu K, Duanmu D, Qiu BS. Expansion of bilin-based red light sensors in the subaerial desert cyanobacterium Nostoc flagelliforme. Environ Microbiol 2022; 24:2047-2058. [PMID: 35172392 DOI: 10.1111/1462-2920.15932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022]
Abstract
Light is the crucial environmental signal for desiccation-tolerant cyanobacteria to activate photosynthesis and prepare for desiccation at dawn. However, the photobiological characteristics of desert cyanobacteria adaptation to one of the harshest habitats on Earth remain unresolved. In this study, we surveyed the genome of a subaerial desert cyanobacterium Nostoc flagelliforme and identified two phytochromes and seven cyanobacteriochromes (CBCRs) with one or more bilin-binding GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains. Biochemical and spectroscopic analyses of 69 purified GAF-containing proteins from recombinant phycocyanobilin (PCB), biliverdin or phycoerythrobilin-producing Escherichia coli indicated that nine of these proteins bind chromophores. Further investigation revealed that 11 GAFs form covalent adducts responsive to near-UV and visible light: eight GAFs contained PCB chromophores, three GAFs contained biliverdin chromophores and one contained the PCB isomer, phycoviolobilin. Interestingly, COO91_03972 is the first-ever reported GAF-only CBCR capable of sensing five wavelengths of light. Bioinformatics and biochemical analyses revealed that residue P132 of COO91_03972 is essential for chromophore binding to dual-cysteine CBCRs. Furthermore, the complement of N. flagelliforme CBCRs is enriched in red light sensors. We hypothesize that these sensors are critical for the acclimatization of N. flagelliforme to weak light environments at dawn.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Jie Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chao Cheng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ren-Han Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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11
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Huo D, Li H, Cai F, Guo X, Qiao Z, Wang W, Yu G, Li R. Genome Evolution of Filamentous Cyanobacterium Nostoc Species: From Facultative Symbiosis to Free Living. Microorganisms 2021; 9:microorganisms9102015. [PMID: 34683336 PMCID: PMC8539589 DOI: 10.3390/microorganisms9102015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 11/16/2022] Open
Abstract
In contrast to obligate bacteria, facultative symbiotic bacteria are mainly characterized by genome enlargement. However, the underlying relationship of this feature with adaptations to various habitats remains unclear. In this study, we used the global genome data of Nostoc strains, including 10 novel genomes sequenced in this study and 26 genomes available from public databases, and analyzed their evolutionary history. The evolutionary boundary of the real clade of Nostoc species was identified and was found to be consistent with the results of polyphasic taxonomy. The initial ancestral species of Nostoc was demonstrated to be consistent with a facultative symbiotic population. Further analyses revealed that Nostoc strains tended to shift from facultative symbiosis to a free-living one, along with an increase in genome sizes during the dispersal of each exterior branch. Intracellular symbiosis was proved to be essentially related to Nostoc evolution, and the adaptation of its members to free-living environments was coupled with a large preference for gene acquisition involved in gene repair and recombination. These findings provided unique evidence of genomic mechanisms by which homologous microbes adapt to distinct life manners and external environments.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China
| | - Fangfang Cai
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiaoyu Guo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyi Qiao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China;
| | - Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Gongliang Yu
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- Correspondence: (G.Y.); (R.L.); Tel.: +86-027-68780067 (G.Y.); +86-027-68780080 (R.L.); Fax: +86-027-68780123 (G.Y.)
| | - Renhui Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325000, China
- Correspondence: (G.Y.); (R.L.); Tel.: +86-027-68780067 (G.Y.); +86-027-68780080 (R.L.); Fax: +86-027-68780123 (G.Y.)
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12
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Gao X, Liu L, Cui L, Zheng T, Ji B, Liu K. Characterization of two β-galactosidases LacZ and WspA1 from Nostoc flagelliforme with focus on the latter's central active region. Sci Rep 2021; 11:18448. [PMID: 34531460 PMCID: PMC8445988 DOI: 10.1038/s41598-021-97929-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022] Open
Abstract
The identification and characterization of new β-galactosidases will provide diverse candidate enzymes for use in food processing industry. In this study, two β-galactosidases, Nf-LacZ and WspA1, from the terrestrial cyanobacterium Nostoc flagelliforme were heterologously expressed in Escherichia coli, followed by purification and biochemical characterization. Nf-LacZ was characterized to have an optimum activity at 40 °C and pH 6.5, different from that (45 °C and pH 8.0) of WspA1. Two enzymes had a similar Michaelis constant (Km = 0.5 mmol/liter) against the substrate o-nitrophenyl-β-D-galactopyranoside. Their activities could be inhibited by galactostatin bisulfite, with IC50 values of 0.59 µM for Nf-LacZ and 1.18 µM for WspA1, respectively. Gel filtration analysis suggested that the active form of WspA1 was a dimer, while Nf-LacZ was functional as a larger multimer. WspA1 was further characterized by the truncation test, and its minimum central region was found to be from residues 188 to 301, having both the glycosyl hydrolytic and transgalactosylation activities. Finally, transgenic analysis with the GFP reporter protein found that the N-terminus of WspA1 (35 aa) might play a special role in the export of WspA1 from cells. In summary, this study characterized two cyanobacterial β-galactosidases for potential applications in food industry.
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Affiliation(s)
- Xiang Gao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China. .,School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Litao Liu
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Lijuan Cui
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Tao Zheng
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ke Liu
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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13
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Zhang ZC, Wang K, Hao FH, Shang JL, Tang HR, Qiu BS. New types of ATP-grasp ligase are associated with the novel pathway for complicated mycosporine-like amino acid production in desiccation-tolerant cyanobacteria. Environ Microbiol 2021; 23:6420-6432. [PMID: 34459073 DOI: 10.1111/1462-2920.15732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Mycosporine-like amino acids (MAAs) were widespread in diverse organisms to attenuate UV radiation. We recently characterized the large, complicated MAA mycosporine-2-(4-deoxygadusolyl-ornithine) in desert cyanobacterium Nostoc flagelliforme. Synthesis of this MAA requires the five-gene cluster mysABDC2C3. Here, bioinformatic analysis indicated that mysC duplication within five-gene mys clusters is strictly limited to drought-tolerant cyanobacteria. Phylogenic analysis distinguished these duplicated MysCs into two clades that separated from canonical MysCs. Heterologous expression of N. flagelliforme mys genes in Escherichia coli showed that MysAB produces 4-deoxygadusol. The ATP-grasp ligase of MysC3 catalyses the linkage of the δ- or ε-amino group of ornithine/lysine to 4-deoxygadusol, yielding mycosporine-ornithine or mycosporine-lysine respectively. The ATP-grasp ligase of MysC2 strictly condenses the α-amino group of mycosporine-ornithine to another 4-deoxygadusol. MysD (D-Ala-D-Ala ligase) functions following MysC2 to catalyse the formation of mycosporine-2-(4-deoxygadusolyl-ornithine). High arginine content likely provides a greater pool of ornithine over other amino acids during rehydration of desiccated N. flagelliforme. Duplication of ATP-grasp ligases is specific for the use of substrates that have two amino groups (such as ornithine) for the production of complicated MAAs with multiple chromophores. This five-enzyme biosynthesis pathway for complicated MAAs is a novel adaptation of cyanobacteria for UV tolerance in drought environments.
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Affiliation(s)
- Zhong-Chun Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Kai Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Fu-Hua Hao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hui-Ru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Contemporary Anthropology, Metabonomics and Systems Biology Laboratory, Fudan University, Shanghai, 200438, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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14
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Oren N, Timm S, Frank M, Mantovani O, Murik O, Hagemann M. Red/far-red light signals regulate the activity of the carbon-concentrating mechanism in cyanobacteria. SCIENCE ADVANCES 2021; 7:7/34/eabg0435. [PMID: 34407941 PMCID: PMC8373116 DOI: 10.1126/sciadv.abg0435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/28/2021] [Indexed: 05/11/2023]
Abstract
Desiccation-tolerant cyanobacteria can survive frequent hydration/dehydration cycles likely affecting inorganic carbon (Ci) levels. It was recently shown that red/far-red light serves as signal-preparing cells toward dehydration. Here, the effects of desiccation on Ci assimilation by Leptolyngbya ohadii isolated from Israel's Negev desert were investigated. Metabolomic investigations indicated a decline in ribulose-1,5-bisphosphate carboxylase/oxygenase carboxylation activity, and this was accelerated by far-red light. Far-red light negatively affected the Ci affinity of L. ohadii during desiccation and in liquid cultures. Similar effects were evident in the non-desiccation-tolerant cyanobacterium Synechocystis The Synechocystis Δcph1 mutant lacking the major phytochrome exhibited reduced photosynthetic Ci affinity when exposed to far-red light, whereas the mutant ΔsbtB lacking a Ci uptake inhibitory protein lost the far-red light inhibition. Collectively, these results suggest that red/far-red light perception likely via phytochromes regulates Ci uptake by cyanobacteria and that this mechanism contributes to desiccation tolerance in strains such as L. ohadii.
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Affiliation(s)
- Nadav Oren
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Stefan Timm
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, Strempelstr. 14, 18057 Rostock, Germany
- Department of Life, Light, and Matter, University of Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany
| | - Oliver Mantovani
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Omer Murik
- Medical Genetics Institute, Shaare Zedek Medical Center, 9103102 Jerusalem, Israel
| | - Martin Hagemann
- Plant Physiology Department, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
- Department of Life, Light, and Matter, University of Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany
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15
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Xu HF, Raanan H, Dai GZ, Oren N, Berkowicz S, Murik O, Kaplan A, Qiu BS. Reading and surviving the harsh conditions in desert biological soil crust: The cyanobacterial viewpoint. FEMS Microbiol Rev 2021; 45:6308820. [PMID: 34165541 DOI: 10.1093/femsre/fuab036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Biological soil crusts (BSCs) are found in drylands, cover ∼12% of the Earth's surface in arid and semi-arid lands and their destruction is considered an important promoter of desertification. These crusts are formed by the adhesion of soil particles to polysaccharides excreted mostly by filamentous cyanobacteria, which are the pioneers and main primary producers in BSCs. Desert BSCs survive in one of the harshest environments on Earth, and are exposed to daily fluctuations of extreme conditions. The cyanobacteria inhabiting these habitats must precisely read the changing conditions and predict, for example, the forthcoming desiccation. Moreover, they evolved a comprehensive regulation of multiple adaptation strategies to enhance their stress tolerance. Here we focus on what distinguishes cyanobacteria able to revive after dehydration from those that cannot. While important progress has been made in our understanding of physiological, biochemical and omics aspects, clarification of the sensing, signal transduction and responses enabling desiccation tolerance are just emerging. We plot the trajectory of current research and open questions ranging from general strategies and regulatory adaptations in the hydration/desiccation cycle, to recent advances in our understanding of photosynthetic adaptation. The acquired knowledge provides new insights to mitigate desertification and improve plant productivity under drought conditions.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Gilat Research Center, Agricultural Research Organization, Mobile Post Negev 2, 8531100 Israel
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Nadav Oren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Simon Berkowicz
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel.,Interuniversity Institute for Marine Sciences in Eilat, P.O.B 469, Eilat, 8810302 Israel
| | - Omer Murik
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
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16
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Chen Z, Shang JL, Hou S, Li T, Li Q, Yang YW, Hess WR, Qiu BS. Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides. Environ Microbiol 2021; 23:5802-5822. [PMID: 33848055 DOI: 10.1111/1462-2920.15521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.
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Affiliation(s)
- Zhen Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jin-Long Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, CA, Los Angeles, 90089, USA
| | - Tao Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Qi Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Yi-Wen Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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17
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Gao X, Jing X, Liu X, Lindblad P. Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy. Mar Drugs 2021; 19:129. [PMID: 33673485 PMCID: PMC7997468 DOI: 10.3390/md19030129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Scytonemin is a promising UV-screen and antioxidant small molecule with commercial value in cosmetics and medicine. It is solely biosynthesized in some cyanobacteria. Recently, its biosynthesis mechanism has been elucidated in the model cyanobacterium Nostoc punctiforme PCC 73102. The direct precursors for scytonemin biosynthesis are tryptophan and p-hydroxyphenylpyruvate, which are generated through the shikimate and aromatic amino acid biosynthesis pathway. More upstream substrates are the central carbon metabolism intermediates phosphoenolpyruvate and erythrose-4-phosphate. Thus, it is a long route to synthesize scytonemin from the fixed atmospheric CO2 in cyanobacteria. Metabolic engineering has risen as an important biotechnological means for achieving sustainable high-efficiency and high-yield target metabolites. In this review, we summarized the biochemical properties of this molecule, its biosynthetic gene clusters and transcriptional regulations, the associated carbon flux-driving progresses, and the host selection and biosynthetic strategies, with the aim to expand our understanding on engineering suitable cyanobacteria for cost-effective production of scytonemin in future practices.
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Affiliation(s)
- Xiang Gao
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xin Jing
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xufeng Liu
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
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18
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Chen MY, Teng WK, Zhao L, Hu CX, Zhou YK, Han BP, Song LR, Shu WS. Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation. THE ISME JOURNAL 2021; 15:211-227. [PMID: 32943748 PMCID: PMC7852516 DOI: 10.1038/s41396-020-00775-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.
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Affiliation(s)
- Meng-Yun Chen
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Wen-Kai Teng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Liang Zhao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Chun-Xiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, 430072, Hubei, PR China
| | - Yang-Kai Zhou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, PR China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510632, PR China.
| | - Li-Rong Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, 430072, Hubei, PR China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
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19
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Wang B, Yang J, Xu C, Yi L, Wan C. Dynamic expression of intra‐ and extra‐cellular proteome and the influence of epiphytic bacteria for
Nostoc flagelliforme
in response to rehydration. Environ Microbiol 2020; 22:1251-1264. [DOI: 10.1111/1462-2920.14931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Bing Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Jingjing Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Chen Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Lanxing Yi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Cuihong Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
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20
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Chen Z, Jiang H, Gao K, Qiu B. Acclimation to low ultraviolet‐B radiation increases photosystem I abundance and cyclic electron transfer with enhanced photosynthesis and growth in the cyanobacterium
Nostoc sphaeroides. Environ Microbiol 2019; 22:183-197. [DOI: 10.1111/1462-2920.14836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/18/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Zhen Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative BiologyCentral China Normal University Wuhan Hubei 430079 People's Republic of China
| | - Hai‐Bo Jiang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative BiologyCentral China Normal University Wuhan Hubei 430079 People's Republic of China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental ScienceXiamen University Xiamen Fujian 361005 People's Republic of China
| | - Bao‐Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative BiologyCentral China Normal University Wuhan Hubei 430079 People's Republic of China
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21
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Oren N, Raanan H, Kedem I, Turjeman A, Bronstein M, Kaplan A, Murik O. Desert cyanobacteria prepare in advance for dehydration and rewetting: The role of light and temperature sensing. Mol Ecol 2019; 28:2305-2320. [DOI: 10.1111/mec.15074] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Nadav Oren
- Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel
| | - Hagai Raanan
- Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel
- Environmental Biophysics and Molecular Ecology Program, Institute of Earth, Ocean and Atmospheric Sciences Rutgers University New Brunswick New Jersey
| | - Isaac Kedem
- Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel
| | - Adi Turjeman
- The Center for Genomic Technologies The Hebrew University of Jerusalem Jerusalem Israel
| | - Michal Bronstein
- The Center for Genomic Technologies The Hebrew University of Jerusalem Jerusalem Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel
| | - Omer Murik
- Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel
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22
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Xu HF, Dai GZ, Qiu BS. Weak red light plays an important role in awakening the photosynthetic machinery following desiccation in the subaerial cyanobacterium Nostoc flagelliforme. Environ Microbiol 2019; 21:2261-2272. [PMID: 30895692 DOI: 10.1111/1462-2920.14600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 11/28/2022]
Abstract
The subaerial cyanobacterium Nostoc flagelliforme can survive for years in the desiccated state and light exposure may stimulate photosynthetic recovery during rehydration. However, the influence of light quality on photosynthetic recovery and the underlying mechanism remain unresolved. Exposure of field collected N. flagelliforme to light intensity ≥2 μmol photons m-2 s-1 showed that the speed of photosystem II (PSII) recovery was in the following order: red > green > blue ≈ violet light. Decreasing the light intensity showed that weak red light stimulated PSII recovery during rehydration. The chlorophyll fluorescence transient and oxygen evolution activity indicated that the oxygen evolution complex (OEC) was the activated site triggered by weak red light. The damaged D1 protein accumulated in the thylakoid membrane during dehydration and is degraded and resynthesized during dark rehydration. PsbO interaction with the thylakoid membrane was induced by weak red light. Thus, weak red light plays an important role in triggering OEC photoactivation and the formation of functional PSII during rehydration. In its arid habitats, weak red light could stimulate the awakening of dormant N. flagelliforme after absorbing water from nighttime dew or rain to maximize growth during the early daylight hours of the dry season.
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Affiliation(s)
- Hai-Feng Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Guo-Zheng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Bao-Sheng Qiu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
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