Different Regulatory Modes of
            <i>Synechocystis</i>
            sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions

Cho, Sang-Hyeok; Jeong, Yu‐Jin; Hong, Seong-Joo; Lee, Hookeun; Choi, Hyung‐Kyoon; Kim, Dong‐Myung; Lee, Choul-Gyun; Cho, Suhyung; Cho, Byung-Kwan

doi:10.1128/msystems.00943-21

Cited by 10 publications

(7 citation statements)

References 62 publications

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“…In our analysis we included 691 and 957 intrinsic termination sites predicted by TERMITe in E. coli based on the data described in this study and Choe et al (17), respectively; 635, 1165, 984 and 1214 sites of B. subtilis based on data from Chhabra et al (15), Mandell et al (7), Dar et al (14) and Mondal et al (8), respectively; 796 terminators from E. faecalis (14); 862 terminators from L. monocytogenes (14); 206 terminators from Z. mobilis (24); 165 terminators from Synechocystis sp . (16); 629 terminators from S. coelicolor (20), 573 terminators from S. venezuelae (20); 520 terminators from S. tsukubensiis (20); 737 terminators from S. griseus (22); 495 terminators from S. lividans (20); 435 terminators from S. clavuligerus (21); 707 terminators from S. avermitilis (20) (Supplementary Figure 3A). All of the above-listed terminators have been identified using TERMITe as described in the Methods section.…”

Section: Resultsmentioning

confidence: 99%

“…follow a bimodal distribution. It was previously suggested that such distribution is related to the evolution of two distinct mechanisms of transcription termination (Rho-dependent and Rho-independent/intrinsic) (16, 21, 22). Thus, the observed bimodality might suggest that the Rho-dependent mechanism might be utilized more often in the GC-rich Streptomyces genus than in other bacteria, having less GC-rich genomes, which is in agreement with the observed lowest fraction of intrinsic terminators among all identified 3’ RNA termini.…”

Section: Discussionmentioning

confidence: 99%

“…Term-seq has been successfully applied to multiple bacterial and archaeal species, including B. subtilis (6–8, 14, 15), Listeria monocytogenes (14), Enterococcus faecalis (14), Synechocystis sp . (16), E. coli (17), Streptomyces sp . (18–22), Pseudomonas aeruginosa (23), Zymomonas mobilis (24), Methanosarcina mazei , and Sulfolobus acidocaldarius (25).…”

Section: Introductionmentioning

confidence: 99%

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Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

Kosiński,

Ranaweera,

Chełkowska-Pauszek

et al. 2024

Preprint

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In recent years, Term-seq became a standard experimental approach for high-throughput identification of 3′ ends of bacterial transcripts. It was widely adopted to study transcription termination events and 3′ maturation of bacterial RNAs. Despite widespread utilization, a universal bioinformatics toolkit for comprehensive analysis of Term-seq sequencing data is still lacking. Here, we describeTERMITe, a novel method for the identification of stable 3′ RNA ends based on bacterial Term-seq data.TERMITeworks with data obtained from both currently available Term-seq protocols and provides robust identification of the 3′ RNA termini. Unique features ofTERMITeinclude the calculation of the transcription termination efficiency using matched RNA-seq data and the comprehensive annotation of the identified 3′ RNA ends, allowing functional analysis of the results. We have appliedTERMITeto the comparative analysis of experimentally validated intrinsic terminators spanning different species across the bacterial domain of life, revealing substantial differences in their sequence and secondary structure. We also provide a complete atlas of experimentally validated intrinsic transcription termination sites for 13 bacterial species, includingEscherichia coli,Bacillus subtilis,Listeria monocytogenes,Enterococcus faecalis,Synechocystissp.,Streptomyces clavuligerus,Streptomyces griseus,Streptomyces coelicolor,Streptomyces avermitilis,Streptomyces lividans,Streptomyces tsukubaensis,Streptomyces venezuelae, andZymomonas mobilis.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

Kosiński,

Ranaweera,

Chełkowska-Pauszek

et al. 2024

Preprint

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“…Both temperature and UVR stress can lead to increased production of ROS, potentially generating oxidative stress. The antioxidant enzyme SOD responds rapidly by catalyzing the conversion of superoxide radicals into H 2 O 2 that is then converted to H 2 O by CAT ( Rastogi et al, 2014 ; Cho et al, 2021 ). In this study, cells grown at elevated temperature showed higher SOD and CAT activity than that at 25°C, and the subsequent exposure with UVR further stimulated the activity of both antioxidases, indicating their protective role in mitigating harmful effects of oxidative stress caused by UVR.…”

Section: Discussionmentioning

confidence: 99%

UV radiation and temperature increase alter the PSII function and defense mechanisms in a bloom-forming cyanobacterium Microcystis aeruginosa

Yan,

Li,

Zang

et al. 2024

Front. Microbiol.

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The aim was to determine the response of a bloom-forming Microcystis aeruginosa to climatic changes. Cultures of M. aeruginosa FACHB 905 were grown at two temperatures (25°C, 30°C) and exposed to high photosynthetically active radiation (PAR: 400–700 nm) alone or combined with UVR (PAR + UVR: 295–700 nm) for specified times. It was found that increased temperature enhanced M. aeruginosa sensitivity to both PAR and PAR + UVR as shown by reduced PSII quantum yields (Fv/Fm) in comparison with that at growth temperature (25°C), the presence of UVR significantly exacerbated the photoinhibition. M. aeruginosa cells grown at high temperature exhibited lower PSII repair rate (Krec) and sustained nonphotochemical quenching (NPQs) induction during the radiation exposure, particularly for PAR + UVR. Although high temperature alone or worked with UVR induced higher SOD and CAT activity and promoted the removal rate of PsbA, it seemed not enough to prevent the damage effect from them showing by the increased value of photoinactivation rate constant (Kpi). In addition, the energetic cost of microcystin synthesis at high temperature probably led to reduced materials and energy available for PsbA turnover, thus may partly account for the lower Krec and the declination of photosynthetic activity in cells following PAR and PAR + UVR exposure. Our findings suggest that increased temperature modulates the sensitivity of M. aeruginosa to UVR by affecting the PSII repair and defense capacity, thus influencing competitiveness and abundance in the future water environment.

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“…We collected transcription termination sites (TTSs) defined by published genome-wide studies [4,[27][28][29][30][31][32][33][34][35] (Table S1). Naively training models on experimentally verified TTS presented several challenges.…”

Section: Data Collection Augmentation and Context-aware Model Trainingmentioning

confidence: 99%

Conserved 3' Stem-Loop Structures Enable Comprehensive Analysis of Bacterial Transcription Termination in Metagenomes, Regardless of Rho Factor Dependency

Jin,

Cui,

et al. 2023

Preprint

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Transcription terminators mark the 3’ ends of both coding and noncoding transcripts in bacteria and play crucial roles in gene regulations (such as controlling the stoichiometry of gene expression and conditionally switching off gene expression by inducing premature termination). Recently developed experimental 3’ end mapping techniques greatly improved the current understanding of bacteria transcription termination, but these methods cannot detect transcripts that are unexpressed in the limited experimental conditions and cannot utilize the vast amount of information embedded in the rapidly growing metagenome data. Computational approaches can relieve these problems, but the development of suchin-silicomethods lags behind the experimental techniques. Previous computational tools are limited to predicting rho-independent terminators (RITs) and are primarily optimized for a few model species. The prediction of rho-dependent terminators (RDTs) which lack obvious consensus sequence patterns, and terminators in diverse non-model bacteria species still presents significant challenges.To address these challenges, we introduce BATTER (BActeriaTranscriptThree primeEndRecognizer), a computational tool for predicting both RITs and RDTs in diverse bacteria species that allows metagenome-scale scanning. We developed a data augmentation pipeline by leveraging available high throughput 3’ end mapping data in 17 bacteria species, and a large collection of 42,905 species-level representative bacteria genomes. Taking advantage context sensitive natural language processing techniques, we trained a BERT-CRF model, using both local features and context information for tagging terminators in genomic sequences.Systematic evaluations demonstrated our model’s superiority: at a false positive rate of 0.1/kilobase, BATTER achieves a sensitivity of 0.924 for predictingE. coliRDTs; and a sensitivity of 0.756 for predicting terminators on term-seq dataset of oral microbiome, outperforming the best existing tool by 0.153. Based on BATTER’s predictions, we systematically analyzed the clade-specific properties of bacteria terminators. The practical utility of BATTER was exemplified through two case studies: identifying functional transcripts from metatranscriptome data and discovering candidate noncoding RNAs related to antimicrobial resistance. As far as we know, BATTER is the first tool simultaneously predicting RITs and RDTs in diverse bacteria species. BATTER is available athttps://github.com/lulab/BATTER.

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Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions

Cited by 10 publications

References 62 publications

Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

UV radiation and temperature increase alter the PSII function and defense mechanisms in a bloom-forming cyanobacterium Microcystis aeruginosa

Conserved 3' Stem-Loop Structures Enable Comprehensive Analysis of Bacterial Transcription Termination in Metagenomes, Regardless of Rho Factor Dependency

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