Summary of Vibrio cholerae O1 biovar El Tor str. N16961, version 28.0

Tier 2 Curated Database

Database Authors: Brendan Wilson-Mortier¹, Amanda Mackie¹, Lisa Moore¹, Ron Caspi², Anamika Kothari², Suzanne Paley², Ian T Paulsen¹, Peter D Karp²

¹Macquarie University, ²SRI International

Summary:
The Vibrionaceae are a globally distributed and diverse family of heterotrophic marine motile bacteria which are either free living, commensal, or opportunistic pathogens of marine animals, with a smaller number adapted to brackish or freshwater environments [Takemura14]. Nearly all members of this family are capable of chitin metabolism and are commonly found attached to the chitinous shells of marine invertebrates but can also be found in associations with marine plants, microalgae, macroalgae, coral, and in the guts of fish [Meibom04, Takemura14, Preheim11]. Additionally, most bioluminescent marine microbes are members of this family and are, via stable symbioses, responsible for the bioluminescent displays of various marine organisms [Takemura14].

Vibrio cholerae, a Gram-negative facultative anaerobe, is arguably the most well-known of the Vibrionaceae due to being the causative agent of the potentially fatal diarrheal disease cholera [Legros18]. Typically caused by the consumption of contaminated food and water sources, cholera epidemics and pandemics remain a significant threat in nations with limited healthcare and unsafe drinking water [Reidl02, Legros18]. The characteristic symptoms of cholera are caused by two main virulence factors, the toxin co-regulated pilus (TCP) and the cholera toxin (CT) [Faruque98, Vanden07]. The CT is encoded within the genome of CTXφ, a filamentous lysogenic bacteriophage which is found integrated into the genome of all toxigenic Vibrio cholerae strains [Waldor96, Reidl02, Faruque02].

There are over 200 serogroups of Vibrio cholerae, yet only two (O1 and O139) are associated with pandemics, whilst serogroup O1 is also composed of strains with two distinct biotypes, Classical, and El Tor. The first six cholera pandemics were caused by Classical biotypes of serogroup O1 whilst the El Tor biotype is responsible for the ongoing seventh pandemic, which originated in Indonesia in 1961 [Feng08, Mukhopadhyay14]. The El Tor strain was originally isolated in 1905 from the gut of pilgrims in a Sinai Peninsula quarantine camp called El Tor, from which the strain got its name [Cvjetanovic72]. By the 1970s it had reached much of Asia and parts of Africa, the Middle East, and Southern Europe; cholera outbreaks in the Americas in the 1990s, Haiti (2010-2019), and more recently Yemen (2015-present) are also part of the seventh pandemic [Cvjetanovic72, Mukhopadhyay14, Federspiel18].

The genome used for this PGDB is an updated version of the first Vibrio cholerae genome sequenced in Bangladesh in 1975 which was isolated from a 7th pandemic El Tor biotype designated Vibrio cholerae O1 biovar El Tor str. N16961 [Heidelberg00, Mutreja11]. As with other Vibrio cholerae strains, and many other members of the Vibrionaceae, the genome of Vibrio cholerae O1 biovar El Tor str. N16961 possesses two circular chromosomes; chromosome 1 encodes most essential genes and is larger (in this strain, 2.96 Mb) than chromosome 2 (in this strain, 1.07 Mb), which evidence suggests may have once been a megaplasmid [Okada05, Sozhamannan20]. In this strain, one copy of CTXφ is integrated within Chromosome 1, but variations in the target chromosome, gene arrangement and copy number are observed between biotypes [Heidelberg00, Sanchez08, Safa20].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 26.0 and MetaCyc [Caspi20] version 26.0 on 15-Dec-2021, and was improved by manual curation, bringing it to a tier 2 status. Some of the data in this PGDB were obtained from publications describing closely related strains, including Vibrio cholerae O1 C6706 [Weng21].

Development of this PGDB was supported by BioCyc subscription revenues and by grant GM080746 from the National Institute of Health.

Taxonomic Lineage: cellular organisms, Bacteria <bacteria>, Pseudomonadota, Gammaproteobacteria, Vibrionales, Vibrionaceae, Vibrio, Vibrio cholerae, Vibrio cholerae O1, Vibrio cholerae O1 biovar El Tor, Vibrio cholerae O1 biovar El Tor str. N16961

Synonyms: Vibrio cholerae O1 biovar El Tor str. N16961

Unification Links: BIOSAMPLE:SAMEA104223503, NCBI BioProject:PRJNA224116, NCBI-Taxonomy:243277

Organism or Sample Properties
Annotation Provider:	NCBI RefSeq
Annotation Pipeline:	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version:	5.0
Annotation Comment:	Best-placed reference protein set; GeneMarkS-2+

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link

Chromosome 1	2,703	2,551	137	15	2,961,182	NCBI-GenBank:NZ_LT906614
Chromosome 2	1,039	1,013	12	14	1,072,319	NCBI-GenBank:NZ_LT906615

Total:	3,742	3,564	149	29	4,033,501

Ortholog data available?	Yes

Genes:	3,744
Pathways:	315
Enzymatic Reactions:	1,614
Transport Reactions:	137
Polypeptides:	3,571
Protein Complexes:	194
Enzymes:	1,009
Transporters:	335
Compounds:	1,101
Transcription Units:	2,466
tRNAs:	98
Growth Media:	1
Transcriptional Regulation:	161
Protein Features:	11,573
GO Terms:	46,015
Gene Essentiality Datasets:	1