INTRODUCTION TO CYANOCYC

CyanoCyc is a portal to cyanobacterial Pathway/Genome Databases (PGDBs) encompassing the vast diversity of the cyanobacteria phylum.

CyanoCyc is integrated with the larger collection of MetaCyc and BioCyc databases, regularly updated multiple times a year, and includes the suite of sophisticated yet easy-to-use bioinformatics Pathway Tools (PTools).

The PTools software (free to academics) can be installed at your site to perform comparisons with existing PGDBs and to create BioCyc-like databases for your own genomes of interest.

CyanoCyc Database Collection

There are more than 270 cyanobacteria PGDBs, five of which are curated:

• PCC 6803 substr. Kazusa
• Synechococcus elongatus PCC 7942
• Synechococcus sp. WH8102
• Prochlorococcus marinus SS120
• Prochlorococcus marinus MED4

A list of all of the cyanobacterial PGDBs can be found in a public Cyanobacteria SmartTable that you can copy and save to your own My SmartTables. Go to Public SmartTables and filter on “cyanobacteria”.

All of the CyanoCyc PGDBs are created from three sources of information:

• Annotated genome: These are generally pulled from NCBI RefSeq and specified on the Summary Statistics home page for each organism.
• Computational Inferences: The PTools software is used to predict reactions and pathways, genes coding for missing enzymes in metabolic pathways, transcription units, protein complexes and transport reactions.
• Imported data: Information from a variety of other databases, such as Protein Features and Gene Ontology information from UniProt.

The curated cyanobacteria PGDBs (Tier 2) contain concise summaries on gene and pathway information pages written by experienced curators with extensive biochemistry and cyanobacteria backgrounds thus ensuring high quality and accurate information from peer-reviewed publications of cyanobacteria research. The kind of information covered includes descriptions of gene functions, experimental evidence, citations as well as information in highly structured database fields that can be searched and compared between organisms within CyanoCyc and the broader BioCyc collection enabling new discoveries.

Bioinformatics Tools

A suite of easy-to-use tools (see Tools dropdown menu) provides extensive search, visualization and analysis capabilities, including omics data analysis, comparative genomics and comparative pathway analyses.

Enhancements for CyanoCyc:

• Find your cyanobacterium of interest: Cyanobacterial taxonomic nomenclature is an evolving field, making it challenging to find strains under old names. CyanoCyc, like all of BioCyc, uses the same taxonomic classifications found in NCBI Taxonomy Browser, but we have also provided older names as synonyms to help you find the cyanobacterial strains in which you are interested.
  • For example, strains of Cyanothece spp. that were split into different genera can be found using the new name, old name, or strain numbers when searching in Change Current Database:
    
  • You can find a detailed tutorial for how to change the current database here.
  • Please be aware that if you search by taxonomy, NCBI taxonomy is used; cyanobacteria can be found Bacteria->Terrabacteria group -> Cyanobacteria/Melainabacteria group.
  • If a synonym is missing, please let us know via our User Feedback Form or by emailing biocyc-support@sri.com
• Select cyanobacteria based on phenotypes: Being able to easily select strains within a phenotypic category, such as all N₂-fixing cyanobacteria, or cyanobacteria representing phenotypic diversity, we have provided SmartTables that list cyanobacteria by phenotype.
  • Cyanobacteria List: Unicellular Cyanobacteria
  • Cyanobacteria List: Representative Cyanobacteria
  • Cyanobacteria List: Picocyanobacteria
  • Cyanobacteria List: Heterocyst Formers
  • Cyanobacteria List: Filamentous Organisms
  • Cyanobacteria List: Nitrogen Fixing Organisms
  • Cyanobacteria List: Obligate Symbionts

  There are various comparative tools that can be carried out on multiple organisms, all of which use the Specify List of Organism Databases pop-up menu. Detailed instructions for its use can be found here.

Other bioinformatics tools for enhancing research:

• Omics Data Analysis: Tools include statistical over-representation analysis, and visualization of gene expression, proteomics, or metabolomics data on metabolic-chart diagrams and on the Omics Dashboard. More information can be found at Omics Data Analysis
• Sequence Pattern Search:This tool allows the user to search for amino acid or nucleotide sequences of interest. A tutorial on how to do this can be found here.
• Pathway Collages: Tools -> Metabolism -> Pathway Collages; This powerful visualization tool allows the user to specify sets of pathways (up to 100) for an organism and customize them in a variety of ways. Omics data can also be overlayed on the different pathways.
• Comparative Analysis Tools: A variety of tools available for comparative analyses are accessible from various locations within a PGDB:
  • Tools -> Analysis -> Comparative Analysis in order to compute statistical tables related to various data types within a single PGDB or between multiple PGDBs
  • Tools -> Analysis -> Comparative Genome Dashboard allows for rapid visualization of the overall biological capabilities of a set of organisms based on their respective genome and pathway annotations, thus facilitating quick identification and exploration of similarities and differences between organisms.
  • Comparison Operations under the OPERATIONS panel to the right of most information pages (e.g. gene or pathway). The operations enable comparisons such as searching for the object type in multiple databases, showing orthologs in multiple databases, aligning genes in a Multi-Genome Browser, aligning nucleotide or amino acid sequences with orthologs
  • Under object specific Tools -> Search for Gene, Proteins, or RNAs, for Compounds, for Reactions and for Pathways, the top search option is Search across multiple organisms/databases
  • Tools -> Search -> Sequence Pattern Match allows the user to search peptide sequences between 3-20 amino acids across full proteomes of up to 70 PGDBs
• Tools for Aligning Sequences: There are a variety of ways to align nucleotide or amino acid sequences for genes or proteins on BioCyc:
  • Under the OPERATIONS panel to the right of gene/protein information pages, there are three tools to align nucleotide or amino acid sequences, one of which allows for alignment of multiple genomes (see below)
  • Align in MultiGenome Browser: This tool enables a user to align a gene of interest to other organisms and provide the genome context surrounding the genes for each organism as seen in an example here. This powerful tool can be found under Comparison Operations in the Operations panel to the right of a gene information page. Detailed instructions for how to use the tool can be found here , as well as specific instructions for selecting a gene of interest here. Instructions for Changing Organisms/Databases for Future Comparison Operations are the same as presented above for Specify List of Organism Databases.
  • Tools -> Analysis -> Multiple Sequence Alignment
  • From a SmartTable containing the genes or proteins you wish to align, you can use either of the following commands found in the OPERATIONS panel at the right of the SmartTable:
    • Column → View Alignment of Gene Nucleotide Sequences
    • Column → View Alignment of Gene Product Peptide Sequences

How to Learn More about BioCyc and PTools

The following information exists about the BioCyc site:

• Guided Tour: Examples of data present in BioCyc
• Webinars: Interactive online seminars describing how to use BioCyc
• Website User's Guide: Instructions for using the BioCyc Website
• BioCyc User Guide: Information about the data content of BioCyc DBs
• PGDB Concepts Guide: The ideas behind BioCyc
• Publications: Articles about BioCyc databases and the Pathway Tools software

More About Cyanobacteria

There are lots of amazing websites devoted to cyanobacteria. Here are links to a few of them:

• CyanoWorld, "Community of early career researchers thriving for innovation and openness in the field of cyanobacteria",https://www.cyano.world , on YouTube at https://www.youtube.com/c/cyanoworld, Linkedin and Twitter @CyanoWorld1
• Cyanosite, "a general webserver for cyanobacterial research" with lots of great links, images and culture media recipes, among other things, https://www-cyanosite.bio.purdue.edu/
• CyanoBase, the original cyanobacteria genome database starting with Synechocystis PCC 6803, https://genome.microbedb.jp/cyanobase/
• JGI Genome Portal for cyanobacteria https://genome.jgi.doe.gov/portal/cyanobacteria/cyanobacteria.info.html
• IMG/ProPortal, full of information about Prochlorococcus, https://img.jgi.doe.gov/cgi-bin/proportal/main.cgi
• Cyanorak, an information system dedicated to visualizing, comparing and curating the genomes of marine picocyanobacteria, http://cyanorak.sb-roscoff.fr/. http://cyanorak.sb-roscoff.fr/cyanorak/
• EPA's Cyanobacteria harmful algal blooms information site, https://www.epa.gov/cyanohabs

Engage With Us

Let us know what you think about CyanoCyc!

• Feedback: Please provide suggestions for improvements of the site or tools, to let us know if something is not working properly, point out errors in the databases, or point out taxonomic synonyms not provided or an important publication we missed in one of the curated cyanobacteria PGDBs.
• Suggest new cyanobacteria for inclusion to CyanoCyc. We are especially interested in covering the vast diversity of cyanobacteria. Please let us know if there are cyanobacteria not yet included. It should already have an annotated genome (preferably in RefSeq - provide its RefSeq accession number).
• Adopt a Cyanobacteria PGDB - Resources are limited, particularly for curation of PGDBs. Read about how you could contribute your time and expertise.
• General user support can always be sent to biocyc-support@sri.com

Credits - the CyanoCyc Advisory Committee

We would like to thank the members of the CyanoCyc advisory committee who have helped us with developing the community focused portal to the cyanobacteria PGDBs within the BioCyc collection:

Alejandro Torrado, Plant Biochemistry and Photosynthesis Institute, University of Seville
Amanda Shelton, Biosphere Sciences & Engineering, Carnegie Institution for Science
Bin Long, Department of Plant Pathology and Microbiology, Texas A&M University
Danny Ducat, Department of Biochemistry & Molecular Biology, Michigan State University
Devaki Bhaya, Biosphere Sciences & Engineering, Carnegie Institution for Science
Erik Zinser, Department of Microbiology, University of Tennessee, Knoxville
Harvey Hou, Department of Physical and Forensic Sciences, Alabama State University
Jeffrey Elhai, Associate Professor, Virginia Commonwealth University
John Casey, Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory
Jonathan Zehr, Distinguished Professor of Ocean Sciences, University of California, Santa Cruz
Zhenxiong "Shaun" Jiang, Department of Microbiology, Miami University