CRISPR-Cas mediated genome engineering of cyanobacteria

Enzymatic assembly of DNA molecules up to several hundred kilobases

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Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria

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The new frontier of genome engineering with CRISPR-Cas9

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Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

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CRISPR-Cas systems for editing, regulating and targeting genomes

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A One Pot, One Step, Precision Cloning Method with High Throughput Capability

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CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

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Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing

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RNA-guided DNA insertion with CRISPR-associated transposases

Strecker, J. G., Ladha, A., Gardner, Z., Schmid-Burgk, J. L., Makarova, K. S., Koonin, E. V., & Zhang, F. (2019) · Science · doi:10.1126/science.aax9181 · Cited by 696 · see citing works

Annotation and Classification of CRISPR-Cas Systems

Makarova, K. S., & Koonin, E. V. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2687-9_4 · Cited by 441 · see citing works

Target specificity of the CRISPR‐Cas9 system

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Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2

Yu, J., Liberton, M., Cliften, P. F., Head, R. D., Jacobs, J., Smith, R. D., Koppenaal, D., Brand, J. J., & Pakrasi, H. B. (2015) · Scientific Reports · doi:10.1038/srep08132 · Cited by 372 · see citing works

ATP drives direct photosynthetic production of 1-butanol in cyanobacteria

Lan, E. I., & Liao, J. C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200074109 · Cited by 366 · see citing works

Rerouting Carbon Flux to Enhance Photosynthetic Productivity

Ducat, D. C., Avelar-Rivas, J. A., Way, J. C., & Silver, P. A. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07901-11 · Cited by 362 · see citing works

Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120

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Cpf1 Is a Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria

Ungerer, J., & Pakrasi, H. B. (2016) · Scientific Reports · doi:10.1038/srep39681 · Cited by 308 · see citing works

Circadian Rhythms in Cyanobacteria

Cohen, S., & Golden, S. S. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-15 · Cited by 290 · see citing works

A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology

Xu, X., & Qi, L. S. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.06.037 · Cited by 290 · see citing works

Light-Dependent Electrogenic Activity of Cyanobacteria

Pisciotta, J. M., Zou, Y., & Baskakov, I. V. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010821 · Cited by 267 · see citing works

Multiple Gene Repression in Cyanobacteria Using CRISPRi

Yao, L., Cengic, I., Anfelt, J., & Hudson, E. P. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00264 · Cited by 246 · see citing works

Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO 2

Gao, X., Gao, F., Liu, D., Zhang, H., Nie, X., & Yang, C. (2016) · Energy & Environmental Science · doi:10.1039/c5ee03102h · Cited by 246 · see citing works

High rates of photobiological H2 production by a cyanobacterium under aerobic conditions

Bandyopadhyay, A., Stöckel, J., Min, H., Sherman, L. A., & Pakrasi, H. B. (2010) · Nature Communications · doi:10.1038/ncomms1139 · Cited by 241 · see citing works

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

Wang, T., Guan, C., Guo, J., Liu, B., Wu, Y., Xie, Z., Zhang, C., & Xing, X. (2018) · Nature Communications · doi:10.1038/s41467-018-04899-x · Cited by 237 · see citing works

Synthetic Biology in Cyanobacteria

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CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973

Wendt, K. E., Ungerer, J., Cobb, R. E., Zhao, H., & Pakrasi, H. B. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0514-7 · Cited by 232 · see citing works

CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production

Li, H., Shen, C. R., Huang, C.-H., Sung, L., Wu, M., & Hu, Y. (2016) · Metabolic Engineering · doi:10.1016/j.ymben.2016.09.006 · Cited by 232 · see citing works

Cyanobacteria: Review of Current Potentials and Applications.

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New applications of synthetic biology tools for cyanobacterial metabolic engineering

Santos-Merino, M., Singh, A. K., & Ducat, D. C. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00033 · Cited by 222 · see citing works

Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002

Markley, A. L., Begemann, M. B., Clarke, R., Gordon, G. C., & Pfleger, B. F. (2014) · ACS Synthetic Biology · doi:10.1021/sb500260k · Cited by 212 · see citing works

SnapShot: Class 2 CRISPR-Cas Systems

Makarova, K. S., Zhang, F., & Koonin, E. V. (2017) · Cell · doi:10.1016/j.cell.2016.12.038 · Cited by 193 · see citing works

Newly discovered Synechococcus sp. PCC 11901 is a robust cyanobacterial strain for high biomass production

Włodarczyk, A., Selão, T. T., Norling, B., & Nixon, P. J. (2020) · Communications Biology · doi:10.1038/s42003-020-0910-8 · Cited by 192 · see citing works

CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002

Gordon, G. C., Korosh, T. C., Cameron, J. C., Markley, A. L., Begemann, M. B., & Pfleger, B. F. (2016) · Metabolic Engineering · doi:10.1016/j.ymben.2016.07.007 · Cited by 189 · see citing works

Cyanogate: a modular cloning suite for engineering cyanobacteria based on the plant moclo syntax

Vasudevan, R., Gale, G. A. R., Schiavon, A. A., Puzorjov, A., Malin, J., Gillespie, M. D., Vavitsas, K., Zulkower, V., Wang, B., Howe, C. J., et al. (2019) · Plant Physiology · doi:10.1104/pp.18.01401 · Cited by 189 · see citing works

A compact Cascade–Cas3 system for targeted genome engineering

Csörgő, B., León, L. M., Chau-Ly, I. J., Vasquez-Rifo, A., Berry, J. D., Mahendra, C., Crawford, E. D., Lewis, J. D., & Bondy‐Denomy, J. (2020) · Nature Methods · doi:10.1038/s41592-020-00980-w · Cited by 189 · see citing works

Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes

Stöckel, J., Welsh, E. A., Liberton, M., Kunnvakkam, R., Aurora, R., & Pakrasi, H. B. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711068105 · Cited by 186 · see citing works

Modular engineering for efficient photosynthetic biosynthesis of 1-butanol from CO ₂ in cyanobacteria

Liu, X., Miao, R., Lindberg, P., & Lindblad, P. (2019) · Energy & Environmental Science · doi:10.1039/c9ee01214a · Cited by 167 · see citing works

CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942

Huang, C.-H., Shen, C. R., Li, H., Sung, L.-Y., Wu, M.-Y., & Hu, Y.-C. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0595-3 · Cited by 164 · see citing works

Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex

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Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

Yao, L., Shabestary, K., Björk, S., Asplund‐Samuelsson, J., Joensson, H. N., Jahn, M., & Hudson, E. P. (2020) · Nature Communications · doi:10.1038/s41467-020-15491-7 · Cited by 158 · see citing works

Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach

Sánchez‐Baracaldo, P., Hayes, P. K., & Blank, C. E. (2005) · Geobiology · doi:10.1111/j.1472-4669.2005.00050.x · Cited by 157 · see citing works

Engineering of photosynthetic mannitol biosynthesis from CO2 in a cyanobacterium

Jacobsen, J. H., & Frigaard, N. (2013) · Metabolic Engineering · doi:10.1016/j.ymben.2013.11.004 · Cited by 153 · see citing works

CRISPR-Based Technologies for Metabolic Engineering in Cyanobacteria

Behler, J., Vijay, D., Hess, W. R., & Akhtar, M. K. (2018) · Trends in biotechnology · doi:10.1016/j.tibtech.2018.05.011 · Cited by 138 · see citing works

Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocysti s sp. PCC 6803

Lin, P.-C., Saha, R., Zhang, F., & Pakrasi, H. B. (2017) · Scientific Reports · doi:10.1038/s41598-017-17831-y · Cited by 129 · see citing works

CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein

Scholz, I., Lange, S. J., Hein, S., Hess, W. R., & Backofen, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056470 · Cited by 128 · see citing works

Enhanced production of sucrose in the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Lin, P.-C., Zhang, F., & Pakrasi, H. B. (2020) · Scientific Reports · doi:10.1038/s41598-019-57319-5 · Cited by 124 · see citing works

Diversion of the Long-Chain Acyl-ACP Pool in Synechocystis to Fatty Alcohols through CRISPRi Repression of the Essential Phosphate Acyltransferase PlsX

Kaczmarzyk, D., Cengic, I., Yao, L., & Hudson, E. P. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2017.11.014 · Cited by 120 · see citing works

Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India

Jaiswal, D., Sengupta, A., Sohoni, S. V., Sengupta, S., Phadnavis, A. G., Pakrasi, H. B., & Wangikar, P. P. (2018) · Scientific Reports · doi:10.1038/s41598-018-34872-z · Cited by 120 · see citing works

Expanding the Potential of CRISPR-Cpf1-Based Genome Editing Technology in the Cyanobacterium Anabaena PCC 7120

Niu, T., Lin, G., Xie, L.-R., Wang, Z.-Q., Xing, W., Zhang, J., & Zhang, C. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00437 · Cited by 119 · see citing works

Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol

Li, H., & Liao, J. C. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-4 · Cited by 116 · see citing works

How a cyanobacterium tells time

Dong, G., & Golden, S. S. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.10.003 · Cited by 115 · see citing works

Class 2 CRISPR/Cas: an expanding biotechnology toolbox for and beyond genome editing

Tang, Y., & Fu, Y. (2018) · Cell & Bioscience · doi:10.1186/s13578-018-0255-x · Cited by 112 · see citing works

CyanoBase: a large-scale update on its 20th anniversary

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A Cyanobacterial Circadian Clockwork

Johnson, C. H., Mori, T., & Xu, Y. Q. (2008) · Current Biology · doi:10.1016/j.cub.2008.07.012 · Cited by 102 · see citing works

Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis

Abernathy, M. H., Yu, J., Ma, F., Liberton, M., Ungerer, J. L., Hollinshead, W. D., Gopalakrishnan, S., He, L., Maranas, C. D., Pakrasi, H. B., et al. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0958-y · Cited by 102 · see citing works

Systems and synthetic biology for the biotechnological application of cyanobacteria

Hagemann, M., & Hess, W. R. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.07.008 · Cited by 101 · see citing works

Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803

Liu, D., & Pakrasi, H. B. (2018) · Microbial Cell Factories · doi:10.1186/s12934-018-0897-8 · Cited by 98 · see citing works

Evidence for the widespread distribution of CRISPR-Cas system in the PhylumCyanobacteria

Cai, F., Axen, S. D., & Kerfeld, C. A. (2013) · RNA Biology · doi:10.4161/rna.24571 · Cited by 96 · see citing works

Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel production

Hendry, J. I., Prasannan, C. B., Joshi, A. A., Dasgupta, S., & Wangikar, P. P. (2016) · Bioresource Technology · doi:10.1016/j.biortech.2016.02.128 · Cited by 94 · see citing works

Targeted Repression of Essential Genes To Arrest Growth and Increase Carbon Partitioning and Biofuel Titers in Cyanobacteria

Shabestary, K., Anfelt, J., Ljungqvist, E., Jahn, M., Yao, L., & Hudson, E. P. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00056 · Cited by 89 · see citing works

Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002

Kopka, J., Schmidt, S., Dethloff, F., Pade, N., Berendt, S., Schottkowski, M., Martin, N., Dühring, U., Kuchmina, E., Enke, H., et al. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0741-0 · Cited by 87 · see citing works

Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering

Lin, P.-C., Zhang, F., & Pakrasi, H. B. (2021) · Metabolic Engineering Communications · doi:10.1016/j.mec.2021.e00164 · Cited by 85 · see citing works

A rapid and reliable strategy for chromosomal integration of gene(s) with multiple copies

Gu, P., Yang, F., Su, T., Wang, Q., Liang, Q., & Qi, Q. (2015) · Scientific Reports · doi:10.1038/srep09684 · Cited by 78 · see citing works

Distinct roles of CpcG1 and CpcG2 in phycobilisome assembly in the cyanobacterium Synechocystis sp. PCC 6803

Kondo, K., Geng, X. X., Katayama, M., & Ikeuchi, M. (2005) · Photosynthesis Research · doi:10.1007/s11120-004-7762-9 · Cited by 78 · see citing works

Recent advances in synthetic biology of cyanobacteria

Sengupta, A., Pakrasi, H. B., & Wangikar, P. P. (2018) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-9046-x · Cited by 78 · see citing works

A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801

Jaiswal, D., Sengupta, A., Sengupta, S., Madhu, S., Pakrasi, H. B., & Wangikar, P. P. (2020) · Scientific Reports · doi:10.1038/s41598-019-57051-0 · Cited by 78 · see citing works

Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph

Liu, D., Liberton, M., Yu, J., Pakrasi, H. B., & Bhattacharyya‐Pakrasi, M. (2018) · mBio · doi:10.1128/mbio.01029-18 · Cited by 77 · see citing works

Engineering of a green‐light inducible gene expression system in S ynechocystis sp. PCC 6803

Abe, K., Miyake, K., Nakamura, M., Kojima, K., Ferri, S. R., Ikebukuro, K., & Sode, K. (2013) · Microbial Biotechnology · doi:10.1111/1751-7915.12098 · Cited by 76 · see citing works

CRISPRi-dCas12a: A dCas12a-Mediated CRISPR Interference for Repression of Multiple Genes and Metabolic Engineering in Cyanobacteria

Choi, S. Y., & Woo, H. M. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00091 · Cited by 76 · see citing works

Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non‐stationary 13C metabolic flux analysis

Hendry, J. I., Prasannan, C. B., Ma, F., Möllers, K. B., Jaiswal, D., Digmurti, M. G., Allen, D. K., Frigaard, N., Dasgupta, S., & Wangikar, P. P. (2017) · Biotechnology and Bioengineering · doi:10.1002/bit.26350 · Cited by 74 · see citing works

An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants

Uniyal, A. P., Mansotra, K., Yadav, S. K., & Kumar, V. S. (2019) · 3 Biotech · doi:10.1007/s13205-019-1760-2 · Cited by 69 · see citing works

Enhancing biomass and ethanol production by increasing NADPH production in Synechocystis sp. PCC 6803

Choi, Y., & Park, J. M. (2016) · Bioresource Technology · doi:10.1016/j.biortech.2016.02.056 · Cited by 67 · see citing works

Application of CRISPR Interference for Metabolic Engineering of the Heterocyst-Forming Multicellular Cyanobacterium Anabaena sp. PCC 7120

Higo, A., Isu, A., Fukaya, Y., Ehira, S., & Hisabori, T. (2017) · Plant and Cell Physiology · doi:10.1093/pcp/pcx166 · Cited by 65 · see citing works

Variations in the Rhythms of Respiration and Nitrogen Fixation in Members of the Unicellular Diazotrophic Cyanobacterial Genus Cyanothece

Bandyopadhyay, A., Elvitigala, T. R., Liberton, M., & Pakrasi, H. B. (2012) · PLANT PHYSIOLOGY · doi:10.1104/pp.112.208231 · Cited by 62 · see citing works

Metabolic engineering of a fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for photoautotrophic production of succinic acid

Sengupta, S., Jaiswal, D., Sengupta, A., Shah, S., Gadagkar, S., & Wangikar, P. P. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01727-7 · Cited by 62 · see citing works

Expanding the toolbox for Synechocystis sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters

Ferreira, E. A., Pacheco, C. C., Pinto, F., Pereira, J. A., Lamosa, P., Oliveira, P., Kirov, B., Jaramillo, A., & Tamagnini, P. (2018) · Synthetic Biology · doi:10.1093/synbio/ysy014 · Cited by 59 · see citing works

Tunable Repression of Key Photosynthetic Processes Using Cas12a CRISPR Interference in the Fast-Growing Cyanobacterium Synechococcus sp. UTEX 2973

Knoot, C. J., Biswas, S., & Pakrasi, H. B. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00417 · Cited by 59 · see citing works

Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria

Jeong, Y., Cho, S.-H., Lee, H., Choi, H., Kim, D., Lee, C., Cho, S., & Cho, B. (2020) · Microorganisms · doi:10.3390/microorganisms8121849 · Cited by 58 · see citing works

The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing

Bayat, H., Modarressi, M. H., & Rahimpour, A. (2017) · Current Microbiology · doi:10.1007/s00284-017-1406-8 · Cited by 56 · see citing works

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Tan, X., Hou, S., Song, K., Georg, J., Klähn, S., Lü, X., & Hess, W. R. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1215-8 · Cited by 54 · see citing works

Photosynthetic Co-production of Succinate and Ethylene in a Fast-Growing Cyanobacterium, Synechococcus elongatus PCC 11801

Sengupta, A., Pritam, P., Jaiswal, D., Bandyopadhyay, A., Pakrasi, H. B., & Wangikar, P. P. (2020) · Metabolites · doi:10.3390/metabo10060250 · Cited by 52 · see citing works

Characterization of Stress Responses of Heavy Metal and Metalloid Inducible Promoters in Synechocystis PCC6803

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CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000

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Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes

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Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria

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CRISPR-Cas systems in multicellular cyanobacteria

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Simplicity and complexity in the cyanobacterial circadian clock mechanism

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Metabolic engineering of Synechocystis sp. PCC 6803 for the photoproduction of the sesquiterpene valencene

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Current understanding of the cyanobacterial CRISPR-Cas systems and development of the synthetic CRISPR-Cas systems for cyanobacteria

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Cycling between growth and production phases increases cyanobacteria bioproduction of lactate

Shabestary, K., Hernández, H. P., Miao, R., Ljungqvist, E., Hallman, O., Sporre, E., Branco dos Santos, F., & Hudson, E. P. (2021) · Metabolic Engineering · doi:10.1016/j.ymben.2021.09.010 · Cited by 42 · see citing works

A novel chlorophyll protein complex in the repair cycle of photosystem II

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Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair

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Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria

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