1
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Ohdate K, Sakata M, Maeda K, Sakamaki Y, Nimura-Matsune K, Ohbayashi R, Hess WR, Watanabe S. Discovery of novel replication proteins for large plasmids in cyanobacteria and their potential applications in genetic engineering. Front Microbiol 2024; 15:1311290. [PMID: 38419637 PMCID: PMC10899382 DOI: 10.3389/fmicb.2024.1311290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Numerous cyanobacteria capable of oxygenic photosynthesis possess multiple large plasmids exceeding 100 kbp in size. These plasmids are believed to have distinct replication and distribution mechanisms, as they coexist within cells without causing incompatibilities between plasmids. However, information on plasmid replication proteins (Rep) in cyanobacteria is limited. Synechocystis sp. PCC 6803 hosts four large plasmids, pSYSM, pSYSX, pSYSA, and pSYSG, but Rep proteins for these plasmids, except for CyRepA1 on pSYSA, are unknown. Using Autonomous Replication sequencing (AR-seq), we identified two potential Rep genes in Synechocystis 6803, slr6031 and slr6090, both located on pSYSX. The corresponding Rep candidates, Slr6031 and Slr6090, share structural similarities with Rep-associated proteins of other bacteria and homologs were also identified in various cyanobacteria. We observed autonomous replication activity for Slr6031 and Slr6090 in Synechococcus elongatus PCC 7942 by fusing their genes with a construct expressing GFP and introducing them via transformation. The slr6031/slr6090-containing plasmids exhibited lower copy numbers and instability in Synechococcus 7942 cells compared to the expression vector pYS. While recombination occurred in the case of slr6090, the engineered plasmid with slr6031 coexisted with plasmids encoding CyRepA1 or Slr6090 in Synechococcus 7942 cells, indicating the compatibility of Slr6031 and Slr6090 with CyRepA1. Based on these results, we designated Slr6031 and Slr6090 as CyRepX1 (Cyanobacterial Rep-related protein encoded on pSYSX) and CyRepX2, respectively, demonstrating that pSYSX is a plasmid with "two Reps in one plasmid." Furthermore, we determined the copy number and stability of plasmids with cyanobacterial Reps in Synechococcus 7942 and Synechocystis 6803 to elucidate their potential applications. The novel properties of CyRepX1 and 2, as revealed by this study, hold promise for the development of innovative genetic engineering tools in cyanobacteria.
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Affiliation(s)
- Kazuma Ohdate
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Minori Sakata
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaisei Maeda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yutaka Sakamaki
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaori Nimura-Matsune
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryudo Ohbayashi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Satoru Watanabe
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
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2
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Kling JD, Lee MD, Walworth NG, Webb EA, Coelho JT, Wilburn P, Anderson SI, Zhou Q, Wang C, Phan MD, Fu F, Kremer CT, Litchman E, Rynearson TA, Hutchins DA. Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacterium Synechococcus. Proc Natl Acad Sci U S A 2023; 120:e2315701120. [PMID: 37972069 PMCID: PMC10665897 DOI: 10.1073/pnas.2315701120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures.
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Affiliation(s)
- Joshua D. Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Michael D. Lee
- ZOLL Medical Corporation, Chelmsford, MA01824
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Nathan G. Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Eric A. Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Jordan T. Coelho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Paul Wilburn
- ZOLL Medical Corporation, Chelmsford, MA01824
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
| | - Stephanie I. Anderson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Qianqian Zhou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Chunguang Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Megan D. Phan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Feixue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Colin T. Kremer
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT06269
| | - Elena Litchman
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Global Ecology, Carnegie Institution, Stanford University, Palo Alto, CA94305
| | - Tatiana A. Rynearson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
| | - David A. Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
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Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao JY, Dai X, Xia J, Jin P. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad150. [PMID: 37100754 DOI: 10.1093/jxb/erad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 06/19/2023]
Abstract
Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.
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Affiliation(s)
- Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing Yuan Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoying Dai
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
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Behle A, Dietsch M, Goldschmidt L, Murugathas W, Berwanger L, Burmester J, Yao L, Brandt D, Busche T, Kalinowski J, Hudson E, Ebenhöh O, Axmann I, Machné R. Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis. Nucleic Acids Res 2022; 50:12790-12808. [PMID: 36533444 PMCID: PMC9825172 DOI: 10.1093/nar/gkac1132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
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Affiliation(s)
| | | | - Louis Goldschmidt
- Institut f. Quantitative u. Theoretische Biologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Wandana Murugathas
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lutz C Berwanger
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jonas Burmester
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lun Yao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, Sweden
| | - David Brandt
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, Sweden
| | - Oliver Ebenhöh
- Institut f. Quantitative u. Theoretische Biologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany,Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ilka M Axmann
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Rainer Machné
- To whom correspondence should be addressed. Tel: +49 211 81 12923;
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5
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Bozan M, Popp D, Kallies R, da Rocha UN, Klähn S, Bühler K. Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601. Front Microbiol 2022; 13:1042437. [PMID: 36425037 PMCID: PMC9679502 DOI: 10.3389/fmicb.2022.1042437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 03/14/2024] Open
Abstract
Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.
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Affiliation(s)
- Mahir Bozan
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
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6
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Bolay P, Schlüter S, Grimm S, Riediger M, Hess WR, Klähn S. The transcriptional regulator RbcR controls ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes in the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2022; 235:432-445. [PMID: 35377491 DOI: 10.1111/nph.18139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Oxygenic photosynthesis evolved in cyanobacteria, primary producers of striking ecological importance. Like plants, cyanobacteria use the Calvin-Benson-Bassham cycle for CO2 fixation, fuelled by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). In a competitive reaction this enzyme also fixes O2 which makes it rather ineffective. To mitigate this problem, cyanobacteria evolved a CO2 concentrating mechanism (CCM) to pool CO2 in the vicinity of RuBisCO. However, the regulation of these carbon (C) assimilatory systems is understood only partially. Using the model Synechocystis sp. PCC 6803 we characterized an essential LysR-type transcriptional regulator encoded by gene sll0998. Transcript profiling of a knockdown mutant revealed diminished expression of several genes involved in C acquisition, including rbcLXS, sbtA and ccmKL encoding RuBisCO and parts of the CCM, respectively. We demonstrate that the Sll0998 protein binds the rbcL promoter and acts as a RuBisCO regulator (RbcR). We propose ATTA(G/A)-N5 -(C/T)TAAT as the binding motif consensus. Our data validate RbcR as a regulator of inorganic C assimilation and define the regulon controlled by it. Biological CO2 fixation can sustain efforts to reduce its atmospheric concentrations and is fundamental for the light-driven production of chemicals directly from CO2 . Information about the involved regulatory and physiological processes is crucial to engineer cyanobacterial cell factories.
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Affiliation(s)
- Paul Bolay
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Susan Schlüter
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Samuel Grimm
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Matthias Riediger
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
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7
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Boulias K, Greer EL. Means, mechanisms and consequences of adenine methylation in DNA. Nat Rev Genet 2022; 23:411-428. [PMID: 35256817 PMCID: PMC9354840 DOI: 10.1038/s41576-022-00456-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 12/29/2022]
Abstract
N6-methyl-2'-deoxyadenosine (6mA or m6dA) has been reported in the DNA of prokaryotes and eukaryotes ranging from unicellular protozoa and algae to multicellular plants and mammals. It has been proposed to modulate DNA structure and transcription, transmit information across generations and have a role in disease, among other functions. However, its existence in more recently evolved eukaryotes remains a topic of debate. Recent technological advancements have facilitated the identification and quantification of 6mA even when the modification is exceptionally rare, but each approach has limitations. Critical assessment of existing data, rigorous design of future studies and further development of methods will be required to confirm the presence and biological functions of 6mA in multicellular eukaryotes.
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8
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Hiraoka S, Sumida T, Hirai M, Toyoda A, Kawagucci S, Yokokawa T, Nunoura T. Diverse DNA modification in marine prokaryotic and viral communities. Nucleic Acids Res 2022; 50:1531-1550. [PMID: 35051998 PMCID: PMC8919816 DOI: 10.1093/nar/gkab1292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/30/2021] [Accepted: 12/17/2021] [Indexed: 11/15/2022] Open
Abstract
DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
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Affiliation(s)
- Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shinsuke Kawagucci
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.,Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Taichi Yokokawa
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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9
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Klähn S, Mikkat S, Riediger M, Georg J, Hess WR, Hagemann M. Integrative analysis of the salt stress response in cyanobacteria. Biol Direct 2021; 16:26. [PMID: 34906211 PMCID: PMC8670252 DOI: 10.1186/s13062-021-00316-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.
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Affiliation(s)
- Stephan Klähn
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, Rostock, Germany
| | - Matthias Riediger
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, A.-Einstein-Str. 3, 18059, Rostock, Germany. .,Department Life, Light and Matter, University of Rostock, Rostock, Germany.
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10
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Spät P, Barske T, Maček B, Hagemann M. Alterations in the CO 2 availability induce alterations in the phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2021; 231:1123-1137. [PMID: 34058021 DOI: 10.1111/nph.17423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacteria are the only prokaryotes that perform plant-like oxygenic photosynthesis. They evolved an inorganic carbon-concentrating mechanism to adapt to low CO2 conditions. Quantitative phosphoproteomics was applied to analyze regulatory features during the acclimation to low CO2 conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Overall, more than 2500 proteins were quantified, equivalent to c. 70% of the Synechocystis theoretical proteome. Proteins with changing abundances correlated largely with mRNA expression levels. Functional annotation of the noncorrelating proteins revealed an enrichment of key metabolic processes fundamental for maintaining cellular homeostasis. Furthermore, 105 phosphoproteins harboring over 200 site-specific phosphorylation events were identified. Subunits of the bicarbonate transporter BCT1 and the redox switch protein CP12 were among phosphoproteins with reduced phosphorylation levels at lower CO2 , whereas the serine/threonine protein kinase SpkC revealed increased phosphorylation levels. The corresponding ΔspkC mutant was characterized and showed decreased ability to acclimate to low CO2 conditions. Possible phosphorylation targets of SpkC including a BCT1 subunit were identified by phosphoproteomics. Collectively, our study highlights the importance of posttranscriptional regulation of protein abundances as well as posttranslational regulation by protein phosphorylation for the successful acclimation towards low CO2 conditions in Synechocystis and possibly among cyanobacteria.
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Affiliation(s)
- Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, D-72076, Germany
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
- Department Life, Light and Matter, Interdisciplinary Faculty, University of Rostock, Rostock, D-18059, Germany
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11
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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12
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Walworth NG, Lee MD, Dolzhenko E, Fu FX, Smith AD, Webb EA, Hutchins DA. Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. Mol Biol Evol 2021; 38:927-939. [PMID: 33022053 PMCID: PMC7947765 DOI: 10.1093/molbev/msaa256] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO2, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO2 exposure and were maintained for at least 4.5 years of CO2 selection. After 7 years of CO2 selection, however, m5C methylation levels that initially responded to high-CO2 returned to ancestral, ambient CO2 levels. Concurrently, high-CO2 adapted growth and N2 fixation rates remained significantly higher than those of ambient CO2 adapted cell lines irrespective of CO2 concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO2-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, 98154, USA
| | - Egor Dolzhenko
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Andrew D Smith
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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13
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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14
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Song S, Timm S, Lindner SN, Reimann V, Hess WR, Hagemann M, Brouwer EM. Expression of Formate-Tetrahydrofolate Ligase Did Not Improve Growth but Interferes With Nitrogen and Carbon Metabolism of Synechocystis sp. PCC 6803. Front Microbiol 2020; 11:1650. [PMID: 32760387 PMCID: PMC7372957 DOI: 10.3389/fmicb.2020.01650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022] Open
Abstract
The introduction of alternative CO2-fixing pathways in photoautotrophic organism may improve the efficiency of biological carbon fixation such as minimizing the carbon loss due to photorespiration. Here, we analyzed the effects of creating a formate entry point into the primary metabolism of the cyanobacterium Synechocystis sp. PCC 6803. The formate-tetrahydrofolate ligase (FTL) from Methylobacterium extorquens AM1 was expressed in Synechocystis to enable formate assimilation and reducing the loss of fixed carbon in the photorespiratory pathway. Transgenic strains accumulated serine and 3-phosphoglycerate, and consumed more 2-phosphoglycolate and glycine, which seemed to reflect an efficient utilization of formate. However, labeling experiments showed that the serine accumulation was not due to the expected incorporation of formate. Subsequent DNA-microarray analysis revealed profound changes in transcript abundance due to ftl expression. Transcriptome changes were observed in relation to serine and glycine metabolism, C1-metabolism and particularly nitrogen assimilation. The data implied that ftl expression interfered with the signaling the carbon/nitrogen ratio in Synechocystis. Our results indicate that the expression of new enzymes could have a severe impact on the cellular regulatory network, which potentially hinders the establishment of newly designed pathways.
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Affiliation(s)
- Shanshan Song
- Plant Physiology Department, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Stefan Timm
- Plant Physiology Department, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molekular Plant Physiology, Potsdam-Golm, Germany
| | - Viktoria Reimann
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Eva-Maria Brouwer
- Plant Physiology Department, Institute of Biosciences, University of Rostock, Rostock, Germany
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15
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Wittmiß M, Mikkat S, Hagemann M, Bauwe H. Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:801-813. [PMID: 32311173 DOI: 10.1111/tpj.14773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
The multienzyme glycine cleavage system (GCS) converts glycine and tetrahydrofolate to the one-carbon compound 5,10-methylenetetrahydrofolate, which is of vital importance for most if not all organisms. Photorespiring plant mitochondria contain very high levels of GCS proteins organised as a fragile glycine decarboxylase complex (GDC). The aim of this study is to provide mass spectrometry-based stoichiometric data for the plant leaf GDC and examine whether complex formation could be a general property of the GCS in photosynthesizing organisms. The molar ratios of the leaf GDC component proteins are 1L2 -4P2 -8T-26H and 1L2 -4P2 -8T-20H for pea and Arabidopsis, respectively, as determined by mass spectrometry. The minimum mass of the plant leaf GDC ranges from 1550 to 1650 kDa, which is larger than previously assumed. The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2, respectively, whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts. Isoform GCS-H2 is not present in leaf mitochondria. In the cyanobacterium Synechocystis sp. PCC 6803, GCS proteins concentrations are low but above the complex formation threshold reported for pea leaf GDC. Indeed, formation of a cyanobacterial GDC from the individual recombinant GCS proteins in vitro could be demonstrated. Presence and metabolic significance of a Synechocystis GDC in vivo remain to be examined but could involve multimers of the GCS H-protein that dynamically crosslink the three GCS enzyme proteins, facilitating glycine metabolism by the formation of multienzyme metabolic complexes. Data are available via ProteomeXchange with identifier PXD018211.
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Affiliation(s)
- Maria Wittmiß
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, Schilling-Allee 69, D-18057, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
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16
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Wu D, Wang Y, Xu X. Effects of a Type I RM System on Gene Expression and Glycogen Catabolism in Synechocystis sp. PCC 6803. Front Microbiol 2020; 11:1258. [PMID: 32582132 PMCID: PMC7296061 DOI: 10.3389/fmicb.2020.01258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 01/25/2023] Open
Abstract
Increasing evidence has shown that DNA methylation is involved in gene regulation in prokaryotes. However, there have been very limited reports about the role of DNA methylation in regulation of gene expression and physiological functions in cyanobacteria. In Synechocystis sp. PCC 6803, four genes on the plasmid pSYSX are predicted to encode the type I restriction-methylation system, slr6095 and slr6096 for the M subunit, slr6097 for the S subunit and slr6102 for the R subunit. Compared to the wild type, slr6095, slr6096, and slr6097 mutants lacked the GGm6AN7TTGG/CCAm6AN7TCC methylation in genomic DNA. Transcriptomic analysis indicated that 171 genes were reproducibly up- or down-regulated in all three mutants relative to the wild type. The changed expression of some genes, including sll1356 for glycogen phosphorylase (GlgP), was associated with the loss of GGm6AN7TTGG/CCAm6AN7TCC methylation in the coding regions or the upstream non-coding sequences. Inactivation of slr6095, slr6096, or slr6097 increased the expression of sll1356 and the GlgP activity but lowered the glycogen content. These results indicated that the DNA methylation by a type I RM system could alter the expression of certain genes and physiological functions in Synechocystis sp. PCC 6803.
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Affiliation(s)
- Dongqing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yali Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xudong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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17
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Oliveira PH, Fang G. Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria. Trends Microbiol 2020; 29:28-40. [PMID: 32417228 DOI: 10.1016/j.tim.2020.04.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/19/2020] [Accepted: 04/10/2020] [Indexed: 12/14/2022]
Abstract
An increasing number of studies have reported that bacterial DNA methylation has important functions beyond the roles in restriction-modification systems, including the ability of affecting clinically relevant phenotypes such as virulence, host colonization, sporulation, biofilm formation, among others. Although insightful, such studies have a largely ad hoc nature and would benefit from a systematic strategy enabling a joint functional characterization of bacterial methylomes by the microbiology community. In this opinion article, we propose that highly conserved DNA methyltransferases (MTases) represent a unique opportunity for bacterial epigenomic studies. These MTases are rather common in bacteria, span various taxonomic scales, and are present in multiple human pathogens. Apart from well-characterized core DNA MTases, like those from Vibrio cholerae, Salmonella enterica, Clostridioides difficile, or Streptococcus pyogenes, multiple highly conserved DNA MTases are also found in numerous human pathogens, including those belonging to the genera Burkholderia and Acinetobacter. We discuss why and how these MTases can be prioritized to enable a community-wide, integrative approach for functional epigenomic studies. Ultimately, we discuss how some highly conserved DNA MTases may emerge as promising targets for the development of novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Pedro H Oliveira
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA.
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA.
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18
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Song N, Zhu Y, Cui Y, Lv M, Tang Y, Cui Z, Dang G, Zheng H, Liu S. Vitamin B and Vitamin C Affect DNA Methylation and Amino Acid Metabolism in Mycobacterium bovis BCG. Front Microbiol 2020; 11:812. [PMID: 32390998 PMCID: PMC7188828 DOI: 10.3389/fmicb.2020.00812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
Vitamins are essential nutrients and key cofactors of enzymes that regulate cellular metabolism, and also activate the immune system. Recent studies have shown that vitamin B1 (VB 1) and vitamin C (Vc) can inhibit Mycobacterium tuberculosis growth, but the precise mechanism is still not well understood. In the present study, we have used RNA-sequencing (RNA-seq), liquid chromatography coupled to mass spectrometry (LC-MS) and single-molecule real-time (SMRT) sequencing to analyze the transcriptional, metabolic and methylation profiles of Mycobacterium bovis BCG when treated with VB 1 and Vc. Our results show that, after vitamin treatment, variant metabolites were mainly clustered in pathways related to amino acid metabolism. Treatment with both vitamins significantly up-regulated the gene encoding cysteine synthase A. Additionally, only BCG that was treated with VC showed m4c modifications. Genes harboring this methylation were up-regulated, suggesting that m4c methylation can promote gene transcription to some extent. Overall, this study contributes to the understanding of the effects of VB 1 and VC, and suggests that these vitamins constitute potential anti-tuberculosis drugs.
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Affiliation(s)
- Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yingying Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mingyue Lv
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yiyi Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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19
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Abstract
While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts. ABBREVIATIONS NGS: next-generation sequencing; Repli-seq: replication sequencing; BrdU: 5-bromo-2'-deoxyuridine; TK: thymidine kinase; GCSI: GC skew index; PET: photosynthetic electron transport; RET: respiration electron transport; Cyt b6f complex: cytochrome b6f complex; PQ: plastoquinone; PC: plastocyanin.
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Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture , Tokyo, Japan
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20
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Scholz I, Lott SC, Behler J, Gärtner K, Hagemann M, Hess WR. Divergent methylation of CRISPR repeats and cas genes in a subtype I-D CRISPR-Cas-system. BMC Microbiol 2019; 19:147. [PMID: 31262257 PMCID: PMC6604393 DOI: 10.1186/s12866-019-1526-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background The presence and activity of CRISPR-Cas defense systems is a hallmark of many prokaryotic microorganisms. Here, the distribution of sequences related to the highly iterated palindrome 1 (HIP1) element and the DNA methylation of CGATCG motifs embedded within HIP1 as a vital part of the CRISPR1 repeat sequence was analyzed in the cyanobacterium Synechocystis sp. PCC 6803. Previously suggested functions of HIP1 include organization of chromosomal structure, DNA recombination or gene regulation, all of which could be relevant in CRISPR-Cas functionality. Results The CRISPR1 repeat-spacer array contains more than 50 CGATCG elements that are double-methylated (5mCG6mATCG) by the enzymes M.Ssp6803I and M.Ssp6803III. Hence, more than 200 possible methylation events cluster over a stretch of 3600 bp of double-stranded DNA. Bisulfite sequencing showed that these motifs were highly methylated at the m5CGATCG positions whereas specific motifs within the CRISPR1 cas genes were hypomethylated suggesting a lowered accessibility for the DNA methylase to these regions. Assays for conjugation and CRISPR1-mediated DNA interference revealed a 50% drop in conjugation efficiency in the mutant lacking the 5mC methylation of CGATCG motifs, while the highly efficient DNA interference activity was not affected by the lack of m5CGATCG DNA-methylation, nor was the capability to differentiate between self and non-self targets based on the protospacer adjacent motifs (PAMs) GTA and GTC versus the non-PAM AGC. A third DNA methylation mediated by M.Ssp6803II modifies the first cytosine in the motif GGCC yielding GGm4CC. We found a remarkable absence of GGCC motifs and hence the corresponding methylation over an 11 kb stretch encompassing all the cas genes involved in interference and crRNA maturation but not adaptation of the CRISPR1 system. Conclusions The lack of GGCC tetranucleotides along the CRISPR1 interference and maturation genes supports the reported hybrid character of subtype I-D CRISPR-Cas systems. We report tight and very high 5mC methylation of the CRISPR1 repeat sequences. Nevertheless, cells lacking the 5mC methylation activity were unaffected in their CRISPR1-mediated interference response but the efficiency of conjugation was reduced by 50%. These results point to an unknown role of m5CGATCG DNA-methylation marks in conjugation and DNA transformation.
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Affiliation(s)
- Ingeborg Scholz
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Steffen C Lott
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Juliane Behler
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Katrin Gärtner
- University of Rostock, Institute of Biosciences, Plant Physiology, A.-Einstein-Str. 3, D-18059, Rostock, Germany
| | - Martin Hagemann
- University of Rostock, Institute of Biosciences, Plant Physiology, A.-Einstein-Str. 3, D-18059, Rostock, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany. .,University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104, Freiburg, Germany.
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