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. 2024 Jan 31:15:1340413.
doi: 10.3389/fmicb.2024.1340413. eCollection 2024.

CyanoCyc cyanobacterial web portal

Lisa R Moore  1 , Ron Caspi  1 , Douglas A Campbell  2 , John R Casey  3 , Sophie Crevecoeur  4 , David J Lea-Smith  5 , Bin Long  6 , Naaman M Omar  2 , Suzanne M Paley  1 , Nicolas M Schmelling  7 , Alejandro Torrado  8 , Jonathan P Zehr  9 , Peter D Karp  1
Affiliations

CyanoCyc cyanobacterial web portal

Lisa R Moore et al. Front Microbiol. .

Abstract

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

Keywords: CyanoCyc; bioinformatics; biotechnology; curation; cyanobacteria; database; genomes; metabolism.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Example of page describing a gene, ndbA of Synechocystis sp. PCC 6803, encoding a subunit of a type II NADH Dehydrogenase. URL: https://cyanocyc.org/gene?orgid=GCF_000009725&id=SGL_RS08135. To generate this page online: (1) Open CyanoCyc.org in a web browser. (2) Click button “Change Current Database,” then type “kazusa” into the box under “Select a Database,” and click on “Synechocystis sp. PCC 6803 substr. Kazusa” that appears just beneath, then click OK. (3) Just below and to the right of the “Change Current Database” is the text entry box for searching – type “ndbA” into that box and press Enter to reach the page for that gene.
Figure 2
Figure 2
Example of page describing the metabolite cyanopterin. URL: https://cyanocyc.org/compound?orgid=GCF_000009725&id=CPD-26623. To get to this page: (1) Follow the instructions provided for Figure 1, except enter “cyanopterin” into the Search in Current Database field and press Enter. (2) Several search results are shown; click “cyanopterin” under the Compounds section to go to the metabolite page shown here.
Figure 3
Figure 3
A cellular overview for the cyanobacterium Synechocystis sp. PCC 6803 (URL: https://biocyc.org/overviewsWeb/celOv.shtml?orgid=GCF_000009725) with superimposed omics data from an experiment studying the effect of excess iron on the organism (one time point from GEO dataset # GDS3741, Houot et al., 2007). To generate this figure: (1) Within the Synechocystis sp. PCC 6803 substr. Kazusa PGDB, go to the Tools drop down menu, then select on Cellular Overview underneath the Metabolism section. (2) Once on the Cellular Overview page, click on Import Data from GEO under the OPERATIONS panel to the right of the page. (3) In the pop-up window that opens, enter the GEO dataset # in the Keywords box and press Go to connect to the dataset. (4) Highlight the data to display, such as GSM84561, and press Submit. (5) Change the Colors Scheme, Y-Axis scale and run the Animation using the Omics Control Panel that pops up once the data is overlaid. A flow diagram of these instructions is also available in Supplementary Figure S1; these can be used as a starting off point for displaying other omics data on the Cellular Overview.
Figure 4
Figure 4
The Omics Dashboard data analysis tool showing transcription levels of Synechocystis sp. PCC 6803 genes involved in amino acid biosynthesis from a culture grown with a low amount of sulfur (GEO dataset # GDS3745, Zhang et al., 2008). To generate this figure: (1) Follow instructions for Figure 3 except use the GEO dataset # GDS3745 and highlight rep 1 for time points 1–72 h under sulfate deprivation; press Submit. (2) Select “Export to Dashboard” at the bottom of the Omics Control Panel to open the data in a new browser window. (3) In the Biosynthesis data panel, mouse over the data area for AA Syn and click to open a new window showing the average gene expression data for the enzymes involved in biosynthesis of each amino acid.
Figure 5
Figure 5
A comparative genome browser showing glyA gene orthologs across five cyanobacterial species and the genome context around the glyA orthologs using the “Align in Multi-Genome Browser” tool. URL: https://cyanocyc.org/genbro/ortho.shtml?lead-orgid=GCF_000009725&lead-genes=SGL_RS04690&orgids=GCF_000010625,SS120,SYNEL,GCF_000009725,GCF_000204075. To make this figure: (1) With the Synechocystis sp. PCC 6803 substr. Kazusa PGDB selected as the current database, enter the string “glyA” into the “Search in Current Database” field and press Enter. (2) Choose “Align in Multi-Genome Browser” under the Operations panel on the right-hand side of the gene/protein information page. (3) A window opens allowing the user to “Specify List of Organism Databases” to be used in the alignment. (4) On the left-hand side, enter the name of organism desired, e.g., Microcystis aeruginosa NIES-843, in the field, highlight (if necessary), then click “Add →” to put it into the Current Selection list on the right-hand side. (5). When your list is complete, push the “OK” button at the bottom right to generate the figure.
Figure 6
Figure 6
The comparative genome dashboard for the five manually curated databases listed in Table 1. URL: https://cyanocyc.org/dashboard/genome-dashboard-compare.shtml?orgids=(SS120+MED4+SYNEL+SYNWH8102+GCF_000009725). To get to this page: (1) Within the Synechocystis sp. PCC 6803 substr. Kazusa PGDB, go to the Tools drop down menu, then select “Comparative Genome Dashboard” under the “Analysis” section. (2) Click on “Select Organisms for Comparison to open the “Specify List of Organism Databases” popup. (3) Enter the names of the organisms desired and “Add” to the “Current Selection,” then press “OK.”
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Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. We recognize and appreciate the funding for the following authors: PK, LM, RC, and SP from SRI International; DC acknowledges Canada Research Chair in Phytoplankton Ecophysiology; DL-S acknowledges funding from the Natural Environmental Research Council, UK (NE/X014428), and the Biotechnology and Biological Sciences Research Council, UK (BB/S020365/1). JC acknowledges funding as part of the Lawrence Livermore National Laboratory’s μBiospheres Science Focus Area FWP SCW1039 supported by the Genome Sciences Program of the U.S. Department of Energy’s Office of Biological and Environmental Research. This work was produced under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-JRNL-859262.

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