Update History for: EcoCyc | MetaCyc | BsubCyc | HumanCyc |YeastCyc

BioCyc Update History

This document summarizes the history of updates to BioCyc.

BioCyc PGDB Count Statistics by Year
  2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005
Number of Genomes 20043 20011 18030 18023 17043 14558 10980 9387 7667 5500 2988 2037 1763 1692 1129 1004 505 409 376

 

The statistics for each year pertain to the last BioCyc release in that year.

Release Notes for BioCyc Version 27.5

Released on December 8, 2023.

Version 27.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

Version 27.5 of BioCyc contains 20,043 Pathway/Genome Databases.

Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.

1. Improvements to BioCyc Databases

New Curated Tier 2 Database for Streptococcus pneumoniae D39V

S. pneumoniae is a major human respiratory pathogen that causes several serious diseases, including pneumonia, meningitis, and septicemia. Strain D39 is an historically important strain that is frequently used in studies of pneumococcal disease. This Pathway/Genome Database (PGDB) was built from a strain known as D39V that was sequenced and comprehensively annotated by the Veening group at the University of Groningen (Slager et al. 2018). The database includes imported transcription-start sites, terminators, and ribosome binding sites from (Slager et al. 2018). The database has undergone significant manual curation focusing on key areas of pneumococcal biology (example curated pathways and genes are noted): Curated gene and protein annotations were propagated from Streptococcus pneumoniae D39V to orthologs in the 234 other S. pneumoniae PGDBs in BioCyc, with each PGDB receiving updates to an average of 300 genes or proteins. Propagated data included gene and protein names, protein complex assignments, and the reactions assigned to each protein.

New Curated Tier 2 Database for Klebsiella pneumoniae NTUH-K2044

Like E. coli, K. pneumoniae is a member of the gammaproteobacterial family Enterobacteriaceae. It is recognized by both the Infectious Diseases Society of America (IDSA) and the World Health Organisation (WHO) as an ESKAPE pathogen (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) -— a globally relevant priority list of clinically significant antibiotic-resistant bacteria. Infections caused by K. pneumoniae range from mild to severe and antibiotic-susceptible to extensively drug-resistant, and can include urinary tract infections (UTIs), pneumonia, wound infections, bloodstream infections (BSIs) and liver abscesses, among others. The genome used to build this Pathway/Genome Database (PGDB) belongs to a clinical hypervirulent strain isolated from a patient with a liver abscess and meningitis. Key areas of manual curation for the database include: Curated gene and protein annotations were propagated from Klebsiella pneumoniae pneumoniae NTUH-K2044 to orthologs in the 179 other K. pneumoniae PGDBs in BioCyc, with each PGDB receiving updates to an average of 202 genes or proteins. Propagated data included gene and protein names, protein complex assignments, and the reactions assigned to each protein.

Improvements to the Synechocystis sp. PCC 6803 substr. Kazusa Database

The curated database for Synechocystis sp. PCC 6803 released in Aug 2023 has since been reviewed and updated by a panel of eight cyanobacterial researchers to ensure high-quality data. These researchers, listed as coauthors on the database Summary Statistics page, contributed expertise in fields such as biosynthetic pathways, electron transport reactions, and pilus proteins. Some notable new additions include:

Improvements to the Corynebacterium glutamicum ATCC 13032 Database

We imported 1698 transcription start sites into this database from Pfeifer-Sancar et al. (2013).

Updates to EcoCyc Version 27.5

The EcoCyc data have been curated from 39,425 publications. EcoCyc includes the equivalent of 4012 textbook-pages of mini-review summaries.

For this release of the EcoCyc database, we have curated new pathways and reactions, new functions for existing proteins and small RNAs, and new regulatory interactions:

2. New in the BioCyc Website

Release Notes for BioCyc Version 27.1

Released on August 28, 2023.

Version 27.1 is a minor release that includes updates to the BioCyc website and downloadable data files.

Version 27.1 of BioCyc contains 20,042 Pathway/Genome Databases.

1. Improvements to BioCyc Databases

New Curated Tier 2 Database for Synechocystis sp. PCC 6803 substr. Kazusa

Synechocystis sp. PCC 6803 is a unicellular, non-nitrogen-fixing, freshwater cyanobacterium that was isolated in 1968 from a lake at Berkeley, California. The original strain does not tolerate glucose in the light. However, as the organism is naturally competent and transformable by exogenous DNA, glucose-tolerant substrains allowing photoheterotrophic, mixotrophic, and heterotrophic growth were constructed. A glucose-tolerant (GT) strain known as GT-Kazusa (full name Synechocystis sp. PCC 6803 substr. Kazusa) was sequenced in 1996, making it the first cyanobacterium and the fourth organism to have its chromosome completely sequenced.

In addition to the polyploid chromosome the organism has seven plasmids - four large ones (pSYSM/120 kb; pSYSX/106 kb; pSYSA/103 kb; pSYSG/44 kb) and three small ones (pCA2.4/2.4 kb; pCB2.4/2.4 kb).

Synechocystis sp. PCC 6803 is one of the most extensively studied cyanobacterial species. The biochemical similarities between plant chloroplasts and the organism make it an ideal system for studying the molecular mechanisms underlying stress responses and stress adaptation in higher plants. The cyanobacterium has also been used extensively as a host for metabolic engineering and synthetic biology studies.

This PGDB was constructed from the RefSeq annotation for the chromosome and plasmids and has undergone significant manual curation based on the literature. This work included authoring of summaries and assignment of evidence codes describing the functions of more than 200 genes. Further curation will continue to be performed in the coming months.

A few examples of curated entries include:

Enzymes

Pathways

Updates to MetaCyc Version 27.1

New and Updated Pathways

We have added 23[more info] new pathways to MetaCyc since the last release and revised 1 existing pathway, for a total of 24 new and revised pathways.

Bacterial Biosynthetic Pathways

A new pathway describes the biosynthesis of poly-β-1,6-N-acetyl-D-glucosamine (PNAG), an exopolysaccharide that is a key component of the biofilm matrix of many pathogenic bacteria. Two new pathways describe the biosynthesis of the capsular polysaccharides of the two most important Streptococcus pneumoniae serovars. Another pathway describes the production of UDP-N-acetyl-α-D-mannosamine, a component of many bacterial and archaeal polysaccharides.

Bacterial Degradation Pathways

A new pathway describes the activity of the recently discovered enzyme EC 4.3.1.33, (R)-1-hydroxy-2-aminoethylphosphonate ammonia-lyase, an enzyme with a narrow substrate specificity which expands the range of phosphonates known to be utilized by bacteria. Many Gram-negative bacterial species carry plasmids such as R773, which contains the arsABCD genes for arsenate detoxification (that process is described in arsenate detoxification I). Some organisms, such as E. coli MG1655, do not carry such a plasmid and rely on chromosomal genes, as described by a new pathway for arsenate detoxification. The marine bacterium Pseudoalteromonas sp. CF6-2 can kill a variety of Gram-positive bacteria by attacking their cell-wall peptidoglycan and can use the liberated D-glutamate as its sole carbon and nitrogen source as described in a new D-glutamate degradation pathway. A new pathway describes how bacteria can convert glycine to pyruvate and ammonium, satisfying the need for both carbon and nitrogen (this pathway is also a part of the photorespiration pathway found in higher plants). Another new pathway describes the degradation of the toxic compound methylglyoxal by the enzyme glyoxalase III (officially named EC 4.2.1.130, D-lactate dehydratase), which converts methylglyoxal to (R)-lactate in a single step.

Plant Biosynthetic Pathways

The kavalactones are known for their psychoactive effects and have pharmaceutical potentials for treating anxiety, insomnia and pain. This pathway describes the use of a cloned styrylpyrone methyltransferase from the kava plant to produce kavalactones in E. coli.

Fungal Biosynthetic Pathways

The sphingofungins are a group of structurally related compounds produced by fungi that specifically inhibit EC 2.3.1.50, serine C-palmitoyltransferase, the enzyme that catalyzes the initial step in sphingolipid biosynthesis. This new pathway describes the biosynthesis of sphingofungins B, C, and D by the human pathogenic fungus Aspergillus fumigatus.

Electron Transfer Pathways

We have added four new electron transfer pathways characterized from the opportunistic pathogenic bacterium Staphylococcus epidermidis.

Archaeal Pathways

Tetrahydromethanopterin and tetrahydrosarcinapterin are alternatives to folate used by members of the archaea. A new pathway describes the latter part of the methanogenesis process in organisms that produce tetrahydromethanopterin. Another pathway describes the production of tetrahydrosarcinapterin by the ATP-dependent glutamylation of tetrahydromethanopterin.

Mammalian Pathways

Aspartame is a low-calorie sweetener used extensively worldwide in a wide variety of foods and beverages. A new pathway describes its degradation in the mammalian intestine. Human milk oligosaccharides are abundant carbohydrates fundamental to infant health and development. They account for 11-17% of the milk. More than a hundred different oligosaccharides have been characterized from human milk; a new pathway describes the biosynthesis of the most common ones.

Salvage Pathways

Eukaryotes produce NAD de novo from L-tryptophan. A new eukaryotic pathway describes the phosphorylation of the vitamin B3 compound β-D-ribosylnicotinate (nicotinate riboside), which allows its salvage for production of NAD. Another salvage pathway describes the conversion of 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylate, a degradation product of an intermediate in thiamine diphosphate biosynthesis, back to thiamine diphosphate.

Other Pathways

Aminoacyl-tRNA synthetases join amino acids with their cognate tRNAs in high fidelity reactions that define the genetic code. Most of these enzymes are specific for a particular amino acid. The reaction starts by activation of the amino acid to an adenylate form, which is is initially held noncovalently in the active site before being transferred to the 2' or 3' hydroxyl group of the terminal ribose of the tRNA. The fidelity required to ensure proper protein biosynthesis is estimated to be 1 in 3300. However, many of the enzymes are not specific enough during the adenylation step, resulting in activation of the wrong amino acid at a rate that is too high. To ensure proper protein synthesis, mechanisms known as "editing" exist for the release of misacylated amino acids before they are transferred to the tRNA.

Updated Pathways

The following pathways have been modified to reflect new information that has become available since they were last curated.

Other Improvements

Update of EC Reactions

During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of August 2023) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6698 EC numbers (including internal M numbers).

Updates to EcoCyc Version 27.1

Improvements to the EcoCyc Database

Several new pathways and reactions were added:

Significant upgrades to major nucleotide binding and cell division proteins:

Additional upgrades of note include:

For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

Release Notes for BioCyc Version 27.0

Released on April 12, 2023.

Version 27.0 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

Version 27.0 of BioCyc contains 20031 Pathway/Genome Databases.

Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.

1. Improvements to BioCyc Databases

New Curated Tier 2 Database for Staphylococcus epidermidis RP62A

Staphylococcus epidermidis is known as a dominant commensal microbial species of the human skin and mucous membranes, and can also be found in association with various other mammals. Colonization by S. epidermidis in healthy adults is usually harmless. However, in recent decades, the species has been recognised as a significant cause of opportunistic and sometimes multidrug-resistant nosocomial infections due to its adherence to various types of implanted medical devices—such as prosthetic joints and intravascular catheters—and its subsequent persistence within biofilms.

This PGDB uses the RefSeq annotation of the biofilm-producing and methicillin-resistant strain S. epidermidis RP62A, and has undergone significant manual curation in key areas such as biofilm formation, virulence, electron transport and metabolism. This work included authoring of summaries and assignment of evidence codes describing the functions of more than 100 genes encoding proteins or small RNAs (sRNAs). Additionally, information from manually curated genes with experimental evidence codes in S. epidermidis RP62A was computationally transferred to 58 other S. epidermidis BioCyc PGDBs via ortholog propagation.

A few examples of curated entries include:

New Curated Tier 2 Database for Alteromonas macleodii ATCC 27126

We have curated the type strain of the ubiquitous marine copiotroph, Alteromonas macleodii, known to be an important part of the marine microbial community and increasingly important model organism. The curation was a collaborative effort at a workshop at the University of Haifa, Israel, in Feb 2023. During this "curate-a-thon" 60 proteins had evidence provided from the literature, 42 unique citations were added along with 41 new reactions, 7 new pathways and 1 superpathway, and more than 1000 protein features were imported.

Highlights of the curation include:

Updates to MetaCyc Version 27.0

MetaCyc now contains 3085 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 10,392 textbook-pages of mini-review summaries.

We have added 24 new pathways to MetaCyc since the last release and revised 2 existing pathways, for a total of 26 new and revised pathways.

Bacterial pathways

Archaeal pathways

Fungal pathways

Plant pathways

Metazoan pathways

The following two pathways have been modified to reflect new information that has become available since they were last curated.

Updates to EcoCyc Version 27.0

The EcoCyc data have been curated from 38835 publications. It includes the equivalent of 3844 textbook-pages of mini-review summaries.

Multiple new genes, including two new proteins and several small RNAs, and new functions for existing proteins have been added and curated with summaries for each new gene product and regulatory interactions for the small RNAs with functions identified.

New genes:

New small RNAs added to EcoCyc:

New gene functions curated:

Other updates include:

2. New in the BioCyc Website

Release Notes for BioCyc Version 26.5

Released on December 13, 2022.

Version 26.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

Version 26.5 of BioCyc contains 20028 Pathway/Genome Databases.

Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.

1. Improvements to BioCyc Databases

Staphylococcus aureus aureus NCTC 8325 updated.

This PGDB has undergone a significant curation upgrade since its initial release at the Tier 2 level. Recent updates have focused on a large number of extracellular toxins and other virulence factors which contribute to the recognized pathogenic capacity of the species (see for example alpha-hemolysin, delta-hemolysin and epsilon-cytotoxin). We have also added over 250 small RNA-encoding genes as described by Carroll et al (2016), and updated the curation of many transporters, respiratory enzymes, DNA repair proteins, and stress-response proteins.

Updates to MetaCyc Version 26.5

MetaCyc now contains 3085 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 10,392 textbook-pages of mini-review summaries.

New and Updated Pathways

We have added 22 new pathways to MetaCyc since the last release. We also added one superpathway, for a total of 23 new pathways.

Bacterial Lipopolysaccharide Biosynthetic Pathways

Lipopolysaccharides (LPS) are complex compounds that can be conceptually divided into three parts: lipid A, which anchors LPS into the membrane; the core oligosaccharide, which contributes to membrane stability; and the O-antigen, which is a polysaccharide that extends away from the cell surface. Each part is a complex large molecule on its own. In order to facilitate the representation of their biosyntetic pathways, these complex pathways have been broken into a series of shorter pathways focusing on one aspect of the process, such as lipid A biosynthesis, core oligosaccharide biosynthesis, and O-antigen biosynthesis. For this release we added several pathways describing the last step in the process - the attachment of the O-antigen to the lipid A-core oligosaccharide complex.

Biosynthesis of Polyketide Extender Units

Polyketides are secondary metabolites produced by some bacteria, fungi, plants, and animals. They are usually biosynthesized by polyketide synthase enzymes (PKS) through the decarboxylative condensation of extender units that are derived from malonyl-CoA, in a process similar to fatty acid synthesis. The biosynthesis of some polyketides involves unusual extender units, which are produced by their own specialized pathways. We added new pathways that describe the biosynthesis of three unusual extender units.

Fungal Biosynthetic Pathways

We added four new pathways that describe the biosynthesis of fungal products. Ascomycin is a macrocyclic polyketide produced by Streptomyces hygroscopicus subsp. ascomyceticus that acts as a potent immunosuppressant that prevents T-cell proliferation. The cyathins are a family of compounds produced by fungi belonging to the genus Cyathus (bird's nest fungi), many of which show interesting biological activities. Like the cyathins, the erinacines are based on a cyathane skeleton, but they are modified with a xylose sugar. Many of the erinacines also demonstrate unique biological activities, such as potent stimulating activity for nerve-growth-factor synthesis and agonistic activity towards the kappa opioid receptor. Fumigillin is a meroterpenoid compound produced by the mold Aspergillus fumigatus that has been studied for its anti-angiogenic properties. It also has pharmaceutical potential for the treatment of microsporidiosis, and is the only effective chemical treatment currently available for honey bee nosemiasis, which is caused by parasitic fungi from the Microsporidia phylum.

Bacterial Degradation Pathways.

N-(1-deoxy-D-fructos-1-yl)-L-asparagine (F-Asn) is an Amadori product - a type of compound that is formed spontaneously by the interaction of a reducing sugar (such as glucose and fructose) with a biological amine such as an amino acid, followed by a rearrangement to form a stable ketoamine. F-Asn occurs naturally in substantial quantities in foods, particularly after heating. We added a pathway describing its degradation by bacterial species such as Salmonella enterica, which uses F-Asn as its primary nutrient in the inflamed intestine. Another new pathway describes a cysteine salvage pathway acting on benzylated cysteine. L-canavanine is a plant product that serves as an antimetabolite of L-arginine and is involved in plant defense. Despite its toxicity it serves as a signaling molecule for free-living symbiotic bacteria to onset their symbiosis with the legume plant, and as a nutrient for bacteria living in the rhizosphere.

Other Bacterial Biosynthetic Pathways

The pentitol sugar ribitol is a common component of teichoic acids and capsular polysaccharides of Gram-positive bacteria. The compound is transferred to the growing polymers from its activated form, CDP-ribitol.

Archaeal Pathways

Glycerol dialkyl glycerol tetraether lipids (GDGTs) are a class of membrane lipids synthesized by many archaea (and some bacteria). They are formed by the joining together of two archaeol-type phospholipids, and because they have two hydrophilic head groups, they form a lipid monolayer in the cell membrane instead of a bilayer, making GDGT-producing organisms exceptional among all clades of life. Macrocyclic archaeol phospholipids are generated by the same enzyme that forms GDGTs. However, in this case rather than connecting two archaeol molecules to each other, the enzyme ligates the ends of the two phytanyl chains to each other, cyclyzing the archaeol molecule.

Mammalian Pathways

All mammals appear to operate a glycolysis pathway from fructose at some capacity, but the pathway plays a key role in the metabolism of the naked mole-rat under low oxygen conditions. These animals tolerate hours of extreme hypoxia and survive 18 minutes of total oxygen deprivation (anoxia) without apparent injury. During anoxia, the naked mole-rat switches to anaerobic metabolism fueled by fructose, which is actively accumulated and metabolized to lactate in the brain via a glycolysis pathway.

Icosanoids Biosynthesis

Polyunsaturated fatty acids (PUFAs) can be oxygenated either enzymatically or in free radical-mediated reactions into hundreds of oxygenated species, many of which are mediators of cellular processes. The best-studied classes of these oxygenated mediators are the icosanoids (sometimes spelled eicosanoids). Even though the name is derived from the ancient Greek word eikosi, which means twenty, to signify the 20 carbons present in arachidonate-derives compounds, it is often used for metabolites of 18- and 22-carbon PUFAs. We added several pathways that integrate reactions that form the PUFAs by releasing them from lipids and steroids and reactions that show the most common transformations of those PUFAs into icosanoids.

Superpathways

Cardiolipin is one of the three most common glycerophospholipids found in bacteria. Although MetaCyc already contained several pathways describing cardiolipin biosynthesis, we have added a new superpathway that integrates several of these pathways, as well as pathways forming precursors used in cardiolipin biosynthesis.

Other Improvements

Update of EC Reactions

During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of October 2022) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6658 EC numbers (including internal M numbers).

Updates to EcoCyc Version 26.5

The EcoCyc data have been curated from 42,768 publications. It includes the equivalent of 3825 textbook-pages of mini-review summaries.

We have curated the previously uncharacterized protein, YmdF, based on recent work by Kaleta et al. 2022, which indicates this protein is likely involved in motility, biofilm formation and susceptibility to a variety of antimicrobial agents.

We also curated regulatory interactions for YiaU and YgfI confirming their role as transcription factors, and their regulation of specific processes was described in the summaries.

In this release summaries were added for 58 putative transcription factors that include properties such as their protein family, the domain for DNA binding, some putative processes that they regulate, and how they are regulated (CITS:35880217).

We included five new inactive conformations of transcription factors: AcrR-3,6-diaminoacridine (proflavin), AcrR-rhodamine 6G (RDG), Cbl-thiosulfate, MurR-N-acetyl-D-glucosamine-6-phosphate and AraC-D-fucose.

New DNA-binding consensus sequences for five sigma factors were added.

New structural insights into several proteins involved in cell division were curated, including FtsQBL and FtsA-FtsZ, as well as additional structural characterizations for PsuK, IaaA, and GyrA.

2. New in the BioCyc Website

Release Notes for BioCyc Version 26.1

Released on August 24, 2022.

Version 26.1 is a minor release that includes updates to the BioCyc website and downloadable data files.

Version 26.1 of BioCyc contains 20,011 Pathway/Genome Databases. A total of 11 new genomes were added. Approximately 2500 databases were rebuilt of which approximately 1100 were for HMP (Human Microbiome Project) organisms.

1. Improvements to BioCyc Databases

New Curated Tier 2 Database for Vibrio cholerae O1 El Tor strain N16961

Vibrio cholerae O1 El Tor strain N16961 is a new Tier 2 PGDB for the seventh pandemic O1 El Tor strain N16961. Toxigenic strains of Vibrio cholerae (serogroups O1 and O139), a gram-negative facultative anaerobe, continue to pose a significant threat to human health and safety, evidenced by the ongoing seventh cholera pandemic which began in 1961. This strain was the first fully sequenced V. cholerae genome, and is widely used as a reference strain in studies of the species. This PGDB uses the RefSeq annotation of an updated genome sequence for N16961 (WTSI, 2019), however, gene names and locus tags from the original assembly (Heidelberg et al 2000) have been included.

The PGDB has undergone significant manual curation. This includes the addition of descriptions summarizing the functions of over 300 proteins and RNAs covering key areas of interest such as virulence, biofilm formation, transcriptional regulation, quorum sensing, transporters, secretion systems, cyclic-di-GMP signalling, chemosensory systems, polysaccharide production, toxin-antitoxin systems and small RNAs.

A few examples of curated entries include:

2. Improvements to MetaCyc

MetaCyc now contains 3,063 metabolic pathways.

The MetaCyc data were curated from 73,000 publications.

New and Updated Pathways

We have added 56 new pathways to MetaCyc since the last release and revised 16 pathways by modifying pathway diagrams, adding commentary, or updating enzyme and gene information. We also added one superpathway, for a total of 73 new and updated pathways.

The new updated pathways included pathways for bacterial degradation, prokaryotic biosynthesis, antibiotic and toxin biosynthesis, cell components biosynthesis, icosanoids biosynthesis, and photorespiration.

During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of July 2022) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6662 EC numbers (including internal M numbers).

For more details see https://BioCyc.org/metacyc/release-notes.shtml.

3. Improvements to EcoCyc

Highlights of EcoCyc Database Improvements

For more details see https://BioCyc.org/ecocyc/release-notes.shtml.


Release Notes for BioCyc Version 26.0

Released on April 13, 2022.

Version 26.0 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

Version 26.0 of BioCyc contains 20,005 Pathway/Genome Databases.

Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.

1. Improvements to BioCyc Databases

Brucella ovis ATCC 25840 Upgraded to Tier 2 BioCyc database

This α-proteobacterium is a highly contagious veterinary pathogen causing genetic diseases such as epididymitis, in sheep, resulting in significant economic impacts on the sheep industry worldwide. However, it is non-zoonotic, unlike most other Brucella species, such as B. abortus, B. suis and B. melitensis.

This strain of B. ovis contains many pseudogenes and lacks many of the metabolic traits found in other Brucella species, which are thought to contribute to the restricted host range of B. ovis. However, even though some traits are not characteristic of B. ovis, such as erythritol degradation and urea hydrolysis, many of the genes for these traits are present and have been curated. The B. ovis database update included information from more than 75 publications and resulted in the addition of 84 reactions, 15 transport reactions, 64 complexes, and 1043 Gene Ontology (GO) terms. Additionally, when our curated database for B. abortus 2308 contained a curated summary for a protein with an ortholog in B. ovis, that summary was imported from the B. abortus database into the B. ovis database.

Some example entries include:

Updates to four BioCyc Cyanobacteria Databases

Updates to MetaCyc Version 26.0

MetaCyc now contains 3,006 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 10,079 textbook-pages of mini-review summaries.

New and Updated Pathways

We have added 26 new pathways to MetaCyc since the last release and revised 38 pathways by modifying pathway diagrams, adding commentary, or updating enzyme and gene information. We also updated one superpathway, for a total of 65 new and updated pathways.

Pentose sugar degradation in MetaCyc

Pentose sugars, including D-xylose, L-arabinose, and D-arabinose, are metabolized through three main types of pathways. The first type, common in bacteria, uses isomerases, kinases, and epimerases to yield xylulose 5-phosphate, which feeds into the pentose phosphate pathway. In the second type of pathway, which involves reductases and dehydrogenases and is found mainly in yeast and fungi, pentoses are converted into a sugar alcohol, which is then converted to ribulose 5-phosphate or xylulose 5-phosphate, again feeding into the pentose phosphate pathway. The third type is partially analogous to the archaeal non-phosphorylative Entner-Doudoroff pathway variant, and has been sub-classified into three routes. We have expanded our coverage to include all possible pathways and revised our summaries to provide a more comprehensive background.

Glucosinolate biosynthesis in MetaCyc

The glucosinolates are secondary metabolites found in 16 plant families, including agriculturally important crop plants of the Brassicaceae such as cabbage, mustard, oilseed rape, and broccoli, as well as the model plant Arabidopsis thaliana, and are responsible for the typical sharp taste and odor of these plants. The configuration of the double bond in the glucosinolate structure has been controversial - some publications report it to be (Z) while others claim it is (E). As a result, the structures in MetaCyc have been inconsistent. We have recently confirmed with experts in the field that all glucosinolates have a (Z) configuration, and have updated all structures and pathways accordingly.

Biosynthesis of compounds of pharmacological importance in MetaCyc

We have curated several pathways for the biosynthesis of secondary metabolites of pharmacological importance.

Other MetaCyc biosynthetic pathways

MetaCyc degradation pathways

D-tagatose is the C-4 epimer of D-fructose. It is a low-calorie natural sugar present in small amounts in fruits and milk products, and can replace sucrose in food. Its low glycemic index and antihyperglycemic effect make D-tagatose a promising sweetener. We added a pathway for its degradation. L-carnitine is a zwitterionic quaternary amine carboxylate that has essential and diverse roles in intermediary metabolism in all living kingdoms, and γ-butyrobetaine is a metabolite involved in the biosynthesis and degradation of L-carnitine. We updated two of the L-carnitine degradation pathways, and expanded our coverage of γ-butyrobetaine degradation from one to three pathways. Glycine betaine is a very efficient osmolyte found in a wide range of bacteria and plants, where it accumulates at high cytoplasmic concentrations in response to osmotic stress to act as an osmoprotectant. We have added a new glycine betaine degradation pathway and revised an existing one. We have also updated pathways for syringate and toluene degradation to reflect new knowledge.

Protein glycosylation in yeast added to MetaCyc

Protein O-mannosylation is an essential protein modification in fungi and animals. In the yeast Saccharomyces cerevisiae mannosyl O-glycans are short oligomannose chains that are attached via a glycosidic bond in α anomeric configuration to the hydroxyl group of Ser or Thr residues. We updated the pathway describing this modification. N-linked glycosylation is an important protein modification in which oligosaccharides are attached to an Asn residue. This type of glycosylation is found in eukaryotes and archaea, and very rarely in bacteria. The pathway leading to the biosynthesis of a tetradecasaccharide precursor is highly conserved, but later processing and elongation steps differ among different organisms. We have added two new pathways that describe late stages of N-glycosylation in yeast. One pathway applies to proteins targeted for retention in cellular organelles, while the other applies to proteins that are destined to the cell wall and to some periplasmic proteins.

Assorted other MetaCyc pathways

EC 6.2.1.1, acetate—CoA ligase, usually converts acetate to acetyl-CoA at the expense of ATP. However, in the bacterium Syntrophus aciditrophicus high diphosphate levels and a high AMP-to-ATP ratio support the operation of the enzyme in the acetate-forming direction, generating ATP. The GABA shunt II pathway describes a route that allows the cyanobacterium Synechocystis sp. PCC 6803 to convert 2-oxoglutarate to succinate, closing an otherwise incomplete TCA cycle. We also updated the pyruvate fermentation to acetate V pathway, which was previously known to occur only in trypanosomatids and some parasitic helminths, to reflect the recent discovery of the pathway in a bacterium.

Other Improvements

Update of EC Reactions:

During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of February 2022) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6621 EC numbers (including internal M numbers).

For more details see https://BioCyc.org/metacyc/release-notes.shtml.

Updates to EcoCyc Version 26.0

The EcoCyc data have been curated from 42,148 publications. It includes the equivalent of 3775 textbook-pages of mini-review summaries.

EcoCyc Modeling Tab Contains Predictions from E. coli Whole Cell Model

This version of EcoCyc contains predictions from computer simulations of an E. coli cell from the E. coli whole-cell modeling project. The aim of the project is to build a computational representation of an E. coli cell that fully captures the dynamics of every known molecule within an E. coli cell, using a heterogeneous set of parameters that are curated from decades of research conducted on this model microbe. The model ties together multiple submodels that each represent a particular domain of an E. coli cell, using the mathematical framework that is most appropriate for the given domain. Macklin et al., 2020 provides more details on how the model was constructed and how its outputs were validated.

The predictions are present on the new Modeling tab on EcoCyc gene pages (example). The Modeling tab contains predictions of the cellular copy numbers for the mRNA and protein product of that gene under three conditions of E. coli growth: aerobic and anaerobic growth under M9 medium with 0.4% glucose, and aerobic growth under M9-derived rich medium. The presented data were calculated by running a batch of computer simulations of an E. coli cell.

Through a collaborative effort between the EcoCyc team and the whole-cell modeling project team at Stanford, we have built a pipeline that allows the whole-cell model to import a subset of the required input parameters, which includes genome annotations, RNA/protein sequences, metabolic reaction networks, transcription factor networks, and reaction stoichiometries, directly from the latest release of the EcoCyc database. With each updated release of EcoCyc, a new batch of simulations is initialized with the newly imported parameters from EcoCyc, and the outputs from the updated simulations are reported on the modeling tabs for EcoCyc gene pages.

The whole-cell model simulates the dynamics of individual cells, which allows it to capture how stochastic processes can lead to heterogeneity between cells that are grown under the same conditions. Thus, in addition to the mean values that are taken from the average of all simulated cells, we are also able to report the standard deviations of each value between the simulated cells, which are presented as error terms in the provided data.

The latest released version of the model code can be accessed for a closer look into the inner workings of the whole-cell model. Please note that the Modeling tab data were generated from the latest working version of the model that contains further updates that may lead to output values that are different from the released version.

Highlights of EcoCyc Database Improvements

For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

2. New in the BioCyc Website

Release Notes for BioCyc Version 25.5

Released on December 15, 2021.

Version 25.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

Version 25.5 of BioCyc contains 19493 Pathway/Genome Databases.

Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.

1. Improvements to BioCyc Databases

New Curated Tier 2 PGDB for Helicobacter pylori 26695

Helicobacter pylori is a Gram-negative bacterium that is often found in the human stomach. It is helix-shaped (giving the genus its name), presumably to help it penetrate the mucoid lining of the stomach and reach the epithelial cells underneath, where it escapes the acidic environment of the stomach.

H. pylori infections are common and usually have no symptoms. In 2015 it was estimated that more than 50% of the world's population is colonized by the bacterium. However, in 10-20% of the cases an infection results in gastritis (stomach inflammation) or ulcers. In some cases the infection may lead to the development of certain cancers. Pathogenicity is correlated with the presence of pathogenicity islands in the genome, though disease outcome depends on additional factors, such as the host's physiology, genotype and dietary habits.

For this release we generated a completely new PGDB for H. pylori 26695, based on the latest available RefSeq annotation. The database underwent significant curation, incorporating data from over 900 publications. Important curated topics include lipopolysaccharide biosynthesis, flagellum biosynthesis, 4 different secretion systems, restriction modification systems, large protein and RNA complexes, and much more. An emphasis was placed on metabolism directly involved in pathogenicity. New pathways were generated to describe the aerobic and anaerobic respiration of the organism, and the biosynthesis of its unique lipopolysaccharides, which contains Lewis (Le) antigens, structures typically found on human epithelial and cancer cells, that allow the organism to evade innate and adaptive immune responses.

A few example entries include:

  • Lactococcus lactis subsp. lactis IL1403 This PGDB has received significant curation upgrades since its initial release at the tier 2 level. Curation from more than 50 additional peer-reviewed publications have resulted in 12 new reactions, 22 imported reactions, 3 new pathways, 81 new and corrected gene names, and 117 summaries for genes, proteins and transporters. Some highlights of the enzymes, reactions and pathways that we have curated:

  • BsubCyc upgrades The BsubCyc PGDB currently contains references to 197 papers published in 2021.
    New curation includes:
  • Updates to MetaCyc Version 25.5

    MetaCyc now contains 2980 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 10757 textbook-pages of mini-review summaries.

    We have added 11 new pathways to MetaCyc since the last release.

    Some highlights of the new additions to MetaCyc include:

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    Updates to EcoCyc Version 25.5

    The EcoCyc data have been curated from 41,490 publications. It includes the equivalent of 3751 textbook-pages of mini-review summaries. Significant updates to EcoCyc include:

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    Release Notes for BioCyc Version 25.1

    Released on August 5, 2021.

    Version 25.1 is a minor release that includes updates to the BioCyc website and downloadable data files.

    Version 25.1 of BioCyc contains 19,535 Pathway/Genome Databases. A total of 1,750 new genomes were added, of which 1710 are for NCBI reference/representative genomes.

    1. Improvements to BioCyc Databases

    Brucella abortus 2308 Upgraded to Curated Tier 2 Database

    This Gram-negative Α-proteobacterium is the causative agent of brucellosis in cattle, resulting in infertility and abortions and significant economic impacts worldwide. It is also a serious zoonotic disease for humans in close contact with or drinking raw milk from infected animals. Brucella abortus is a facultative intracellular pathogen that infects phagocytic cells of the immune system, effectively evading detection. This upgrade has focused on curation of proteins, reactions and metabolic pathways associated with the virulence and immune evasion mechanisms of Brucella abortus 2308. These include O-antigen biosynthesis proteins, a Type IV secretion system (new to BioCyc) with more than a dozen putative T4SS substrates and effector proteins, and more than 50 small RNAs. Additional database upgrades include:

    2. Improvements to MetaCyc

    We have added 32 new pathways to MetaCyc since the last release and revised 17 pathways by modifying pathway diagrams, adding commentary, or updating enzyme and gene information. We also updated two superpathways, for a total of 51 new and updated pathways. The new pathways fall under the following categories:

    Update of EC Classification

    During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of July 2021) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6563 EC numbers (including internal M numbers).

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    3. Improvements to EcoCyc

    EcoCyc includes the following updates:

  • We have added two new pathways:
  • Three existing metabolic pathways were modified based on new information in the literature:
  • The summaries for 29 transcription factors and 6 sigma factors were updated.

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.


    Release Notes for BioCyc Version 25.0

    Released on May 20, 2021.

    Version 25.0 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 25.0 of BioCyc contains 17,835 Pathway/Genome Databases.

    Chrome and Firefox are the recommended web browsers for BioCyc, followed by Safari and Edge. Web browsers are incompatible, they can treat the same web page differently.
    If you are having difficulties with the new BioCyc release, try doing a hard reload (hold down the Shift key and click the Reload button on your browser); deleting cookies can also help.

    1. Improvements to BioCyc Databases

    Updates to BioCyc Databases

    Updates to MetaCyc Version 25.0

    MetaCyc now contains 2937 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 9739 textbook-pages of mini-review summaries.

    We have added 85 new pathways to MetaCyc since the last release and revised 15 pathways by modifying pathway diagrams, adding commentary, or updating enzyme and gene information. We also added two superpathways, for a total of 102 new and updated pathways.

    Some highlights of the new additions to MetaCyc include:

    Lipopolysaccharide biosynthesis

    The lipopolysaccharides (LPS) are composed of three components – lipid A, the core oligosaccharide, and the O antigen. We have added several pathways that describe the biosynthesis of lipid A and the core oligosaccharides of Brucella species and Porphyromonas gingivalis, and added many pathways for the biosynthesis of O antigens. We now have full coverage of the O antigens produced by Salmonella species, by many Escherichia coli serotypes, and by Brucella abortus, Porphyromonas gingivalis, and some strains of Shigella boydii.

    Other Polysaccharide-Related Biosynthetic Pathways

    We created a new pathway for the biosynthesis of colanic acid, an exopolysaccharide secreted by E. coli and a number of other Enterobacteriaceae. We also revised existing pathways for the biosynthesis of succinoglycan and the enterobacterial common antigen (ECA).

    Arsenic Metabolism

    Arsenic is a natural component of the earth’s crust and is widely distributed throughout the environment in the air, water and land. It exists most commonly in the (III) and (V) oxidation states, and many compounds of both forms are highly toxic. All organisms have developed defense mechanisms to cope with arsenic compounds. In this release we performed an extensive revision of our coverage of arsenic compound metabolism. We now have an up-to-date coverage of all known arsenic-related enzymes in bacteria, yeast, plants and animals.

    Electron Transport in Cyanobacteria

    EC 7.1.1.10, ferredoxin—quinone oxidoreductase (H+-translocating) is a key enzyme in the electron transfer chain of cyanobacteria and plastids that until recently has been mischaracterized. The enzyme couples electron transport from ferredoxin to plastoquinone with proton pumping from the cytoplasm to the thylakoid lumen, and participates in cyclic electron flow, retuning electrons generated by photosystem I to the plastoquinone pool, thus bypassing the generation of reducing power. Based on the new functional characterization of the enzyme we have revised several cyanobacterial electron transport pathways and created a new pathway to describe cyclic electron flow.

    11-oxyandrogens

    A new pathway describes the biosynthesis of 11-oxygenated C19 steroids (11-oxyandrogens). These steroids have long been recognized as major androgens in teleost fishes. However, more recently it has been discovered that they are also produced in humans and play an important role in several disorders such as congenital adrenal hyperplasia (CAH), polycystic ovary syndrome (PCOS), and premature adrenarche.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    Updates to EcoCyc Version 25.0

    The EcoCyc data have been curated from 40,472 publications.

    Significant updates to EcoCyc include:

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    2. New in the BioCyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    Release Notes for BioCyc Version 24.5

    Released on January 7, 2021.

    Version 24.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 24.5 of BioCyc contains 18,030 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    Updates to Other databases

    Chlamydia trachomatis D/UW-3/CX Upgraded to Tier 2 Curated Database

    This reference genome is the first Chlamydia genome in the BioCyc database to be upgraded from Tier 3 to Tier 2. Chlamydia trachomatis, originally named Rickettsia trachomae, are obligate intracellular bacterial pathogens that grow in membrane bound vacuoles within the cytoplasm of their eukaryotic host cells. The strain D/UW-3/CX belongs to serovar D, which is associated with sexually transmitted infections in humans and is the common causative agent of urogenital tract pathologies that can lead to infertility and increased risk of HIV infection. This intracellular pathogen has a reduced genome, is known to utilize host derived carbon/energy sources and is characterized by a unique developmental cycle. This update of Chlamydia trachomatis D/UW-3/CX has focused on curating the proteins and reactions associated with the central metabolic pathways and differential activity associated with distinct phases of the developmental cycle. Database upgrades include:

    BioCyc contains databases for 127 sequenced Chlamydia genomes, 15 of which are representative or reference genomes.

    Updates to MetaCyc Version 24.5

    MetaCyc now contains 2,859 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 10,179 textbook-pages of mini-review summaries.

    We have added and/or updated 15 pathways in MetaCyc since the last release.

    Significant updates to MetaCyc include:

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    Updates to EcoCyc Version 24.5

    The EcoCyc data have been curated from 39,932 publications.

    Significant updates to EcoCyc include:

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    2. New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    Release Notes for BioCyc Version 24.1

    Released on September 8, 2020.

    Version 24.1 is a minor release that includes updates to the BioCyc website and downloadable data files.

    Version 24.1 of BioCyc contains 18,023 Pathway/Genome Databases, of which 1,247 are new genomes and 680 of the PGDBs were re-generated. 1,927 of the PGDBs are for NCBI representative genomes.

    1. Improvements to BioCyc Databases

    Integration of Phenotype Microarray Datasets

    We have added Biolog Phenotype Microarray data to the six BioCyc databases listed below. To navigate to the Phenotype Microarray data in BioCyc, click on a link to an organism page below, then, click on the "List" button in the table row for "Phenotype Microarray Datasets".

    Curation of Acinetobacter baumannii ATCC 17978 Database

    This BioCyc database has been upgraded from Tier 3 to Tier 2. Strain ATCC 17978 presented in this PGDB is from a polymyxin B- resistant substrain of the original, 1951 clinical isolate from a fatal infant meningitis, originally named Moraxella glucidolytica nonliquefaciens. This strain carries two plasmids, which contain some predicted virulence factors, including TonB-dependent receptors. Strain ATCC 17978 is one of the well-studied, multidrug-resistant, pathogenic strains that is responsible for a range of community- and hospital-acquired infections and has been included among the World Health Organizations list of pathogens of major public health concern. For this updated database, we have focused on virulence factors such as those related to metal acquisition systems and outer membrane proteins. Database updates include:

    BioCyc contains databases for 265 sequenced Acinetobacter genomes.

    Updates to Lactobacillus rhamnosus GG Database

    We further refined the Tier 2 PGDB for this organism by performing the following:

    Updates to MetaCyc Version 24.1

    MetaCyc now contains 2,847 metabolic pathways -- we have added or significantly revised 39 pathways in this release.

    MetaCyc contains the equivalent of 10,111 textbook-pages of mini-review summaries.

    Areas of MetaCyc curation for this release include new pathways in the following areas:

    Database links for proteins in MetaCyc have been updated. Previously there were four database names associated with links to ENTREZ ids in MetaCyc: PID, REFSEQ, NCBI-REFSEQ-PRO, and GI. All of these links used ENTREZ identifiers and all are now linked using the database name PID.

    MetaCyc Sequence Files: The sequence files used by the PathoLogic pathway hole-filler have been enhanced to include ids and sequences from ENTREZ in addition to UniProt. These files identify proteins in UniProt and ENTREZ that are associated with different enzyme activities. These files were previously called uniprot-seq-ids.dat and uniprot-seq-ids.seq. The new files, which are available in the MetaCyc flat-file distribution, are now called the following. All of the files are formatted as Lisp lists, actually as a list of lists. Each Lisp list is a series of items enclosed in parentheses.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    Updates to Other E. coli PGDBs in BioCyc 24.1

    To improve the other E. coli PGDBs in BioCyc (meaning those PGDBs describing strains other than K-12 MG1655), we propagated gene and protein annotations from EcoCyc to the 480 other E. coli PGDBs in BioCyc. On average, each of those PGDBs received updates to 2535 gene or proteins. The information we propagated included gene and protein names, protein complex assignments, and the reactions assigned to each protein. Propagation was performed from a gene or protein in EcoCyc only if it had experimental support, and only if the existing annotations for the target gene or protein did not have experimental evidence. The target gene/protein is a computed ortholog of the source gene/protein. The propagation event was recorded in a "history entry" for the target gene/protein that is displayed on the gene/protein page and explains what information was propagated.

    Updates to EcoCyc Version 24.1

    The EcoCyc data have been curated from 39,000 publications.

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    Release Notes for BioCyc Version 24.0

    Released on May 14, 2020.

    Version 24.0 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 24.0 of BioCyc contains 16,817 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    New in MetaCyc Version 24.0

    MetaCyc now contains 2,801 metabolic pathways from all domains of life. MetaCyc contains the equivalent of 9,790 textbook-pages of mini-review summaries.

    We have added and/or updated 49 pathways in MetaCyc since the last release.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    New in EcoCyc Version 24.0

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    2. New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:


    Release Notes for BioCyc Version 23.5

    Released on December 19, 2019.

    Version 23.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 23.5 of BioCyc contains 17,043 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    New in MetaCyc Version 23.5

    MetaCyc now contains 2,766 metabolic pathways. The MetaCyc data were curated from 62,400 publications.

    We have added and/or updated 28 pathways in MetaCyc since the last release.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    New in EcoCyc Version 23.5

    Significant updates to EcoCyc include identification and characterization of YedK as a genome maintenance protein which forms covalent cross-links to abasic (apurinic/apyrimidinic) (AP) sites in ssDNA; identification of the new complex CRP-Sxy, which regulates some genes related to DNA uptake (natural competence); and identification of the HicB protein, known as the antitoxin of the HicA-HicB toxin-antitoxin system, as a transcription factor that autoregulates the transcription of the hicAB operon.

    2. New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:


    Release Notes for BioCyc Version 23.1

    Released on September 19, 2019.

    Version 23.1 is a minor release that includes updates to some of the databases at the BioCyc Web site and the corresponding downloadable data files.

    Version 23.1 of BioCyc contains 14735 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    New in MetaCyc Version 23.1

    MetaCyc now contains 2,749 metabolic pathways. The MetaCyc data were curated from 61,800 publications.

    We have added 27 new pathways to MetaCyc since the last release. In addition, we significantly revised 12 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.


    Release Notes for BioCyc Version 23.0

    Released on April 29, 2019.

    Version 23.0 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 23.0 of BioCyc contains 14,728 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    New in MetaCyc Version 23.0

    MetaCyc now contains 2,722 metabolic pathways. The MetaCyc data were curated from 60,000 publications.

    We have added 23 new pathways to MetaCyc since the last release. In addition, we significantly revised 12 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    New in EcoCyc Version 23.0

    EcoCyc now contains the equivalent of 3,105 textbook-pages of mini-review summaries for genes, pathways, and regulatory interactions.

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    2. New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:


    Release Notes for BioCyc Version 22.6

    Released on December 12, 2018.

    Version 22.6 is a minor release that includes updates to the BioCyc Web site and downloadable data files. This release does not include the downloadable Pathway Tools software; its next release is planned for March 2019.

    Version 22.6 of BioCyc contains 14,560 Pathway/Genome Databases.

    New in MetaCyc Version 22.6

    MetaCyc now contains 2,698 metabolic pathways. The MetaCyc data were curated from 58,954 publications. We have added 12 new pathways to MetaCyc since the last release. In addition, we significantly revised 7 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    New in EcoCyc Version 22.6

    We have added 2 new pathways to EcoCyc since the last release. The EcoCyc data were curated from 36,151 publications.

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    Release Notes for BioCyc Version 22.5

    Released on Sep 25, 2018.

    Version 22.5 is a major release that includes updates to the BioCyc Web site and downloadable data files, and a new version of the downloadable Pathway Tools software.

    Version 22.5 of BioCyc contains 14,560 Pathway/Genome Databases.

    1. Improvements to BioCyc Databases

    New in MetaCyc Version 22.5

    MetaCyc now contains 2,666 metabolic pathways. The MetaCyc data were curated from 58,000 publications.

    We have added 26 new pathways to MetaCyc since the last release. In addition, we significantly revised 19 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information.

    For more details see https://BioCyc.org/metacyc/release-notes.shtml.

    New in EcoCyc Version 22.5

    EcoCyc now contains the equivalent of 3,105 textbook-pages of mini-review summaries for genes, pathways, and regulatory interactions.

    New GenBank File for Escherichia coli K-12 MG1655 Released!

    A new GenBank file of the E. coli K-12 MG1655 genome and annotation (U00096.3) was released on September 24, 2018. The updated genome annotation in this file was directly generated from EcoCyc Version 22.5 in a collaboration with Guy Plunkett III (University of Wisconsin), Andrea Auchincloss (UniProt/Swiss-Prot), and NCBI.

    The most recent prior update to U00096.3 was released on August 1, 2014. The version suffix is changed only when the nucleotide sequence has changed -- thus the version number remains the same for this new release because no changes have been made to the nucleotide sequence. This new update does contain a large number of other changes based on publications in the past four years. The most significant updates include:

    Highlights of EcoCyc Database Improvements

    For more details see https://BioCyc.org/ecocyc/release-notes.shtml.

    2. New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:


    3. BioCyc Operations -- Monitoring the Error Log

    Despite the extensive testing that we perform prior to every BioCyc and Pathway Tools release, software bugs appear in every new released version. An essential tool for helping us to identify and fix these bugs as quickly as possible is the BioCyc error log. Whenever an error occurs in our website, the software "catches" the error and records various information in a log file, including the URL of the web page from which the error originated, the error message, and a "stack backtrace". The backtrace is a listing of the procedure calls in progress at the time the error occurred -- a snapshot of the internal state of the software.

    Our programming team receives an email each night containing a summary of the error log, which we inspect to determine what errors are occurring, and with what frequency. We pursue the most frequent errors first. In most cases we are able to fix the problem within a day, and issue a patch that is incorporated by our running web servers, and is loaded by remote users of Pathway Tools the next time they start the software.


    Release Notes for BioCyc Version 22.0

    Released on April 24, 2018.

    New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    New in EcoCyc Version 22.0

    The EcoCyc data were curated from 33,000 publications.

    Highlights of EcoCyc Database Improvements

    For more details see http://BioCyc.org/ecocyc/release-notes.shtml.

    New in MetaCyc Version 22.0

    MetaCyc now contains 2,609 metabolic pathways; the MetaCyc data were curated from 55,000 publications.

    We have added 37 new pathways to MetaCyc since the last release. In addition, we significantly revised 8 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information, for a total of 45 new and updated pathways.

    For more details see http://BioCyc.org/metacyc/release-notes.shtml.

    Improvements to other BioCyc Databases in Version 22.0


    Release Notes for BioCyc Version 21.5

    Released on November 28, 2017.

    New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    New in EcoCyc Version 21.5

    The EcoCyc data were curated from 33,000 publications.

    Highlights of EcoCyc Database Improvements

    For more details see http://BioCyc.org/ecocyc/release-notes.shtml.

    New in MetaCyc Version 21.5

    MetaCyc now contains 2,609 metabolic pathways; the MetaCyc data were curated from 55,000 publications.

    We have added 37 new pathways to MetaCyc since the last release. In addition, we significantly revised 8 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information, for a total of 45 new and updated pathways.

    For more details see http://BioCyc.org/metacyc/release-notes.shtml.

    Improvements to other BioCyc Databases in Version 21.5

    Use wget to Download BioCyc Files

    Our users are reporting frequent interruptions when downloading large BioCyc data files. Please use wget rather than a web browser to download large BioCyc files. wget uses longer timeouts than web browsers, and also can continue a download that was interrupted from where it left off.


    Release Notes for BioCyc Version 21.1

    Released on August 15, 2017.


    Release Notes for BioCyc Version 21.0

    Released on April 27, 2017.

    New in the Biocyc Website


    Release Notes for BioCyc Version 20.5

    Released on December 17, 2016.

    New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    Significant Curation Updates in Version 20.5

    New in EcoCyc

    New in MetaCyc

    New Pan-Genome Databases in BioCyc

    We created three new pan-genome databases in BioCyc, adding to the Mycobacterium tuberculosis pan-genome database released in the previous version of BioCyc. Each pan-genome database integrates genes and pathways from multiple strains within BioCyc to provide a global view of the genomes available for that species.
    Organism Number of Strains
    Pseudomonas aeruginosa 23
    Peptoclostridum difficile 10
    Listeria monocytogenes 35

    New Gene Essentiality Datasets in BioCyc

    We have loaded additional gene essentiality data from the OGEE database into BioCyc databases. These data were originally published in the primary literature, and were then aggregated by OGEE.

    The following organism databases include the newly added gene essentiality data. To access a given gene essentiality dataset, click on the Growth-Media page for a given organism below, and then click on a growth medium to see a list of all genes that are essential in that medium. In additional, gene pages list essentiality data for that gene when available.

    Organism # Datasets
    Acinetobacter baumannii ATCC 17978 2
    Acinetobacter sp. ADP1 1
    Agrobacterium fabrum C58 1
    Brevundimonas subvibrioides ATCC 15264 1
    Burkholderia cenocepacia J2315 1
    Caulobacter crescentus NA1000 1
    Escherichia coli CFT073 1
    Escherichia coli K-12 substr. MG1655 (EcoCyc 5
    Escherichia coli O25b:H4-ST131 1
    Francisella tularensis novicida U112 2
    Haemophilus influenzae Rd KW20 1
    Helicobacter pylori 26695 2
    Homo sapiens 1
    Mycobacterium tuberculosis H37Rv 4
    Mycoplasma genitalium G37 1
    Mycoplasma pulmonis UAB CTIP 1
    Porphyromonas gingivalis ATCC 33277 1
    Pseudomonas aeruginosa PAO1 2
    Pseudomonas aeruginosa UCBPP-PA14 3
    Rhizobium leguminosarum bv. viciae 3841 1
    Rhodopseudomonas palustris CGA009 1
    Saccharomyces cerevisiae S288c 1
    Salmonella enterica enterica serovar Typhi str. CT18 1
    Salmonella enterica enterica serovar Typhi str. Ty2 1
    Salmonella enterica enterica serovar Typhimurium str. 14028S 4
    Salmonella enterica enterica serovar Typhimurium str. LT2 1
    Salmonella enterica enterica serovar Typhimurium str. SL1344 4
    Shewanella oneidensis MR-1 1
    Sphingomonas wittichii RW1 1
    Staphylococcus aureus aureus NCTC 8325 2
    Streptococcus pneumoniae D39 1
    Streptococcus pneumoniae R6 1
    Streptococcus pneumoniae TIGR4 1
    Synechococcus elongatus PCC 7942 1

    Release Notes for BioCyc Version 20.1

    Released on Sep 29, 2016.

    New Gene Essentiality Datasets in BioCyc

    We have loaded gene essentiality data from the OGEE database into BioCyc databases. These data were originally published in the primary literature, and were then aggregated by OGEE.

    To access a given gene essentiality dataset, click on the Growth-Media page for a given organism below, and then click on a growth medium to see a list of all genes that are essential in that medium. In additional, gene pages list essentiality data for that gene when available.

    Significant Curation Updates in Version 20.1

    New in EcoCyc

    New in MetaCyc

    Release Notes for BioCyc Version 20.0

    Released on May 9th, 2016.

    New in the Biocyc Website

    The following new features are present in the BioCyc website, and are thus available to all databases within the BioCyc collection:

    Significant Curation Updates

    Release Notes for BioCyc Version 19.5

    Released on Nov 12, 2015.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    The MetaFlux metabolic-modeling module has undergone the following enhancements: Full Pathway Tools release notes: http://bioinformatics.ai.sri.com/ptools/release-notes.shtml

    EcoCyc release notes: http://ecocyc.org/release-notes.shtml

    MetaCyc release notes: http://metacyc.org/release-notes.shtml

    Release Notes for BioCyc Version 19.1

    Released on June 24, 2015.

    Version 19.1 of BioCyc contains 5,711 Pathway/Genome Databases.

    This new release includes eight new pathways in EcoCyc.

    MetaCyc now contains 2,363 metabolic pathways and 12,700 reactions; its contents have been curated from over 46,000 publications.

    Release Notes for BioCyc Version 19.0

    Released on March 20, 2015.

    Version 19.0 of BioCyc contains 5,500 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    Transcriptional Regulation Data Imported from RegTransBase and TractorDB

    Full Pathway Tools release notes: http://bioinformatics.ai.sri.com/ptools/release-notes.shtml

    EcoCyc release notes: http://ecocyc.org/release-notes.shtml

    MetaCyc release notes: http://metacyc.org/release-notes.shtml

    Release Notes for BioCyc Version 18.5

    Released on Nov 07, 2014.

    Version 18.5 of BioCyc contains 5,500 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    Full Pathway Tools release notes: http://bioinformatics.ai.sri.com/ptools/release-notes.shtml

    EcoCyc release notes: http://ecocyc.org/release-notes.shtml

    MetaCyc release notes: http://metacyc.org/release-notes.shtml

    Release Notes for BioCyc Version 18.1

    Released on June 23, 2014.

    Version 18.1 of BioCyc contains 3,563 Pathway/Genome Databases.

    Release Notes for BioCyc Version 18.0

    Released on March 24, 2014.

    Version 18.0 of BioCyc contains 3,531 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    Full Pathway Tools release notes: http://bioinformatics.ai.sri.com/ptools/release-notes.shtml

    EcoCyc release notes: http://ecocyc.org/release-notes.shtml

    MetaCyc release notes: http://metacyc.org/release-notes.shtml


    Release Notes for BioCyc Version 17.5

    Released on October 11, 2013.

    Version 17.5 of BioCyc contains 2,988 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    EcoCyc release notes: http://ecocyc.org/release-notes.shtml

    MetaCyc release notes: http://metacyc.org/release-notes.shtml

    Release Notes for BioCyc Version 17.0

    Released on March 29, 2013.

    Version 17.0 of BioCyc contains 2,920 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    Release Notes for BioCyc Version 16.5

    Released on November 15, 2012.

    Version 16.5 of BioCyc contains 2,038 Pathway/Genome Databases.

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software


    Release Notes for BioCyc Version 16.0

    Released on February 16, 2012.

    Version 16.0 of BioCyc contains 1,763 Pathway/Genome Databases, including 414 complete bacterial genomes from the Human Microbiome Project.

    In this release of BioCyc, our E. coli W3110 database has undergone significant enhancements under funding from the PortEco project. We performed an annotation normalization of W3110 with respect to EcoCyc (which describes strain MG1655). The purpose of this project was to modernize the annotation of W3110 with respect to the frequently updated EcoCyc annotation, and to remove spurious differences in annotations between the two strains (e.g., different protein names for proteins having the same function).

    BioCyc Web Site Improvements

    Desktop Mode Improvements to the Downloadable Pathway Tools Software

    Release Notes for BioCyc Version 15.5

    Released on October 21, 2011.

    Version 15.5 of BioCyc contains 1,700 Pathway/Genome Databases, including 414 complete bacterial genomes from the Human Microbiome Project.

    The HumanCyc database has been promoted to a Tier 1 database to reflect the significant curation that HumanCyc has undergone during the last two years, and to reflect the creation of a flux-balance analysis model from HumanCyc.

    BioCyc Web Site Improvements

    Improvements to Desktop BioCyc

    This section describes improvements to the version of BioCyc that runs locally on your desktop computer in conjunction with the Pathway Tools (PTools) software.

    For more details and examples see: