scholarly journals Revisiting the early evolution of Cyanobacteria with a new thylakoid-less and deeply diverged isolate from a hornwort

2021 ◽  
Author(s):  
Nasim Rahmatpour ◽  
Duncan A. Hauser ◽  
Jessica M. Nelson ◽  
Pa Yu Chen ◽  
Juan Carlos Villarreal A. ◽  
...  
Keyword(s):  
Clock Genes ◽  
Atmospheric Oxygen ◽  
Carotenoid Biosynthesis ◽  
Oxygenic Photosynthesis ◽  
Phylogenetic Position ◽  
Closely Related Species ◽  
Gene Sets ◽  
Wide Range ◽  
Circadian Clock Genes ◽  
Carotenoid Biosynthesis Pathway

SummaryCyanobacteria have played pivotal roles in Earth’s geological history especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life—the vast majority of extant diversity belongs to Phycobacteria (or “crown Cyanobacteria”), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here we describe a new culturable member of Gloeobacteria, Anthocerobacter panamensis, isolated from a tropical hornwort. Anthocerobacter diverged from Gloeobacter over 1.4 billion years ago and has low 16S identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerobacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerobacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerobacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.

scholarly journals Alternative splicing of circadian clock genes correlates with temperature in field-grown sugarcane

2019 ◽  
Author(s):  
Luíza L. B. Dantas ◽  
Cristiane P. G. Calixto ◽  
Maira M. Dourado ◽  
Monalisa S. Carneiro ◽  
John W. S. Brown ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Circadian Clock ◽  
Clock Genes ◽  
Genes Expression ◽  
Hybrid Genome ◽  
Wide Range ◽  
Circadian Clock Genes ◽  
Alternatively Spliced ◽  
Complex Hybrid ◽  
Fast Responses

AbstractAlternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95 and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.

scholarly journals The Transcriptional Cycle Is Suited to Daytime N2Fixation in the Unicellular Cyanobacterium “CandidatusAtelocyanobacterium thalassa” (UCYN-A)

mBio ◽  
2018 ◽  
Vol 10 (1) ◽  
Author(s):  
María del Carmen Muñoz-Marín ◽  
Irina N. Shilova ◽  
Tuo Shi ◽  
Hanna Farnelid ◽  
Ana María Cabello ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Clock Genes ◽  
Gene Expression Pattern ◽  
Oxygenic Photosynthesis ◽  
Marine Cyanobacteria ◽  
Symbiotic Interaction ◽  
Unicellular Cyanobacterium ◽  
Content Type ◽  
Algal Host ◽  
Circadian Clock Genes

ABSTRACTSymbiosis between a marine alga and a N2-fixing cyanobacterium (CyanobacteriumUCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related toBraarudosphaera bigelowii. N2-fixing cyanobacteria use different strategies to avoid inhibition of N2fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2only at night, but, surprisingly, UCYN-A appears to fix N2during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N2fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N2fixation in the light, such asTrichodesmiumand heterocyst-forming cyanobacteria, than to those inCrocosphaeraorCyanothecespecies, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N2fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.IMPORTANCEThe symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related toBraarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2evolved through photosynthesis. This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2fixation, which is likely more energetically efficient than fixing N2at night, as found in other unicellular marine cyanobacteria.

scholarly journals A transcriptional cycle suited to daytime N2 fixation in the unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A)

2018 ◽  
Author(s):  
María del Carmen Muñoz-Marin ◽  
Irina N. Shilova ◽  
Tuo Shi ◽  
Hanna Farnelid ◽  
Ana Maria Cabello ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Clock Genes ◽  
Gene Expression Pattern ◽  
Oxygenic Photosynthesis ◽  
Marine Cyanobacteria ◽  
Symbiotic Interaction ◽  
Unicellular Cyanobacterium ◽  
Oxygen Sensitive ◽  
Algal Host ◽  
Circadian Clock Genes

AbstractThe symbiosis between a marine alga and a N2-fixing cyanobacterium (UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated, and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N2-fìxing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but surprisingly UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that transcription patterns in UCYN-A are most similar to marine cyanobacteria that are capable of aerobic N2 fixation in the light such as Trichodesmium and heterocyst-forming cyanobacteria, rather than Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.ImportanceThe symbiotic N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host, which is closely related to Braarudosphaera bigelowii, have been shown to be globally distributed and important in open ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation, but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study shows that the symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as in other unicellular marine cyanobacteria.

scholarly journals Circadian clock: a regulator of the immunity in cancer

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhen Zhang ◽  
Puhua Zeng ◽  
Wenhui Gao ◽  
Qing Zhou ◽  
Ting Feng ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Potential Role ◽  
Clock Genes ◽  
Regulatory Function ◽  
Cancer Immunity ◽  
Wide Range ◽  
Circadian Clock Genes ◽  
Peripheral Clocks ◽  
New Strategies

AbstractThe circadian clock is an endogenous timekeeper system that controls and optimizes biological processes, which are consistent with a master circadian clock and peripheral clocks and are controlled by various genes. Notably, the disruption of circadian clock genes has been identified to affect a wide range of ailments, including cancers. The cancer-immunity cycle is composed of seven major steps, namely cancer cell antigen release and presentation, priming and activation of effector immunity cells, trafficking, and infiltration of immunity to tumors, and elimination of cancer cells. Existing evidence indicates that the circadian clock functions as a gate that govern many aspects of the cancer-immunity cycle. In this review, we highlight the importance of the circadian clock during tumorigenesis, and discuss the potential role of the circadian clock in the cancer-immunity cycle. A comprehensive understanding of the regulatory function of the circadian clock in the cancer-immunity cycle holds promise in developing new strategies for the treatment of cancer.

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

Circadian clock genes as promising therapeutic targets for autoimmune diseases

2021 ◽  
pp. 102866
Author(s):  
Kun Xiang ◽  
Zhiwei Xu ◽  
Yu-Qian Hu ◽  
Yi-Sheng He ◽  
Guo-Cui Wu ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Circadian Clock ◽  
Clock Genes ◽  
Therapeutic Targets ◽  
Circadian Clock Genes

Revision of Coronostrongylus (Nematoda : Strongyloidea) parasitic in the stomachs of macropodid marsupials

2002 ◽  
Vol 16 (6) ◽  
pp. 893 ◽  
Author(s):  
I. Beveridge
Keyword(s):  
Papua New Guinea ◽  
Host Species ◽  
Related Species ◽  
New Guinea ◽  
Nematode Species ◽  
Closely Related Species ◽  
Nematode Genus ◽  
Eastern Australia ◽  
Wide Range ◽  
Species Occurrences

The monotypic nematode genus Coronostrongylus Johnston & Mawson, 1939 from the stomachs of macropodid marsupials was reviewed and was found to consist of a least seven closely related species. Coronostrongylus coronatus Johnston & Mawson, 1939 is found most commonly in Macropus rufogriseus, but occurs occasionally in M. dorsalis, M. parryi and Petrogale inornata. Coronostrongylus johnsoni, sp. nov. is most commonly found in M. dorsalis, but occurs also in M. rufogriseus, M. parma, Thylogale stigmatica, Petrogale godmani and P. brachyotis. Coronostrongylus barkeri, sp. nov. is most prevalent in Onychogalea unguifera, but occurs also in M. rufus, M. robustus and P. brachyotis. Coronostrongylus closei, sp. nov. is restricted to Petrogale persephone. Coronostrongylus sharmani, sp. nov. occurs only in rock wallabies from eastern Australia: P.�coenensis, P. godmani and P. mareeba; C. spratti, sp. nov. occurs in P. inornata and P. assimilis. Coronostrongylus spearei, sp. nov. is restricted to Papua New Guinea where it is found in Dorcopsulus vanhearni, Dorcopsis hageni and D. muelleri. Although all of the nematode species occur in one principal host species or a series of closely related host species, occurrences in geographically disjunct areas and in phylogenetically distant hosts are features of C. coronatus, C. barkeri, sp. nov. and C. johnsoni, sp. nov. The occurrence of seven closely related nematode species found in a wide range of macropodid host species is more readily accounted for by a hypothesis involving multiple colonisations of hosts than by the hypothesis of co-speciation.

scholarly journals Genetic Characterization of the Carotenoid Biosynthetic Pathway in Methylobacterium extorquens AM1 and Isolation of a Colorless Mutant

2003 ◽  
Vol 69 (12) ◽  
pp. 7563-7566 ◽  
Author(s):  
Stephen J. Van Dien ◽  
Christopher J. Marx ◽  
Brooke N. O'Brien ◽  
Mary E. Lidstrom
Keyword(s):  
Biosynthetic Pathway ◽  
Genetic Characterization ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Methylobacterium Extorquens ◽  
Growth Properties ◽  
Carotenoid Biosynthesis Pathway ◽  
Free Strain

ABSTRACT Genomic searches were used to reconstruct the putative carotenoid biosynthesis pathway in the pink-pigmented facultative methylotroph Methylobacterium extorquens AM1. Four genes for putative phytoene desaturases were identified. A colorless mutant was obtained by transposon mutagenesis, and the insertion was shown to be in one of the putative phytoene desaturase genes. Mutations in the other three did not affect color. The tetracycline marker was removed from the original transposon mutant, resulting in a pigment-free strain with wild-type growth properties useful as a tool for future experiments.

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