Database Authors
Varsha Naidu1, Lisa Moore1, Amanda Mackie1, Ron Caspi2, Anamika Kothari2, Pallavi Subhraveti2, Ian T Paulsen1, Peter D Karp2
1Macquarie University, 2SRI International
Summary Lactococcus lactis is a mesophilic, Gram-positive, non-motile, non-spore-forming, facultative anaerobe, previously Streptococcus lactis. It has been used for centuries in the production of fermented food products including cheese, yoghurt, and sauerkraut. It is generally considered homofermentative because it produces (S)-lactate as its primary fermentation product and contains genes for EC 2.7.1.11, 6-phosphofructokinase (pfkA and pfkB). However, it is capable of heterofermentative metabolism due to its ability to produce diacetyl, (S)-acetoin, and acetaldehyde in addition to (S)-lactate. This has made Lactococcus lactis a microorganism of industrial importance [Schleifer85, Kandler83, Platteeuw95].

Lactic acid has multiple industrial applications, which includes its use in the food industry as an acidifier during preservation and as a flavour enhancing agent. Subsequently, metabolic engineering efforts in L. lactis have also led to the production of B vitamins (folate and riboflavin) [Sybesma03, Sybesma03a, Sybesma04], biofuels (ethanol) [Liu16] and therapeutics [Steidler06]. As a result of its industrial importance, L. lactis has been given the status of generally recognized as safe (GRAS) by the Food and Drug Administration (FDA).

Taxonomically, Lactococcus lactis can be subdivided into three subspecies namely, Lactococcus lactis hordniae, Lactococcus lactis lactis (including the biovar Lactococcus lactis lactis bv. diacetylactis), and Lactococcus cremoris cremoris [vanHylckama06, Rademaker07]. Lactococcus lactis has been isolated from a wide variety of environments including plants, animals, and dairy. Strains associated with plant and animal niches can ferment a wide variety of mono-, di- and tri-saccharides [Kelly10, Wels19].

This Pathway/Genome Database (PGDB) is focused on the subspecies Lactococcus lactis lactis IL1403 a plasmid-free derivative of strain IL594, which was originally isolated from a cheese starter culture, and based on the genome sequence from [Bolotin01]. The PGDB was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 25.0 and MetaCyc [Caspi18] version 25.5 on 16-Apr-2021.

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

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0026622,3922,21786892,365,589NCBI Assembly:GCF_000006865.1
Ortholog data available?Yes
Database Contents
Genes2,392
Pathways218
Enzymatic Reactions1,000
Transport Reactions28
Polypeptides2,219
Protein Complexes59
Enzymes567
Transporters195
Compounds714
Transcription Units1,563
tRNAs63
Transcriptional Regulation1
Protein Features9,336
GO Terms19,363
Database Version29.0
Synonyms Lactococcus lactis subsp. lactis str. IL1403
Lactococcus lactis subsp. lactis Il1403
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Streptococcaceae
Lactococcus
Lactococcus lactis
Lactococcus lactis lactis
Lactococcus lactis lactis IL1403
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603339
NCBI BioProjectPRJNA224116
NCBI-Taxonomy272623
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typereference
Copyright 2020, SRI International. All Rights Reserved.

References

Bolotin01: Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A (2001). "The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403." Genome Res 11(5);731-53. PMID: 11337471

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Kandler83: Kandler O (1983). "Carbohydrate metabolism in lactic acid bacteria." Antonie Van Leeuwenhoek 49(3);209-24. PMID: 6354079

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Kelly10: Kelly WJ, Ward LJ, Leahy SC (2010). "Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures." Genome Biol Evol 2;729-44. PMID: 20847124

Liu16: Liu J, Dantoft SH, Wurtz A, Jensen PR, Solem C (2016). "A novel cell factory for efficient production of ethanol from dairy waste." Biotechnol Biofuels 9;33. PMID: 26925162

Platteeuw95: Platteeuw C, Hugenholtz J, Starrenburg M, van Alen-Boerrigter I, de Vos WM (1995). "Metabolic engineering of Lactococcus lactis: influence of the overproduction of alpha-acetolactate synthase in strains deficient in lactate dehydrogenase as a function of culture conditions." Appl Environ Microbiol 61(11);3967-71. PMID: 8526510

Rademaker07: Rademaker JL, Herbet H, Starrenburg MJ, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JE (2007). "Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting." Appl Environ Microbiol 73(22);7128-37. PMID: 17890345

Schleifer85: Schleifer KH, Kraus J, Dvorak C, Kilpper-Balz R, Collins MD, Fischer W (1985). "Transfer of Streptococcus lactis and Related Streptococci to the Genus Lactococcus gen. nov." Systematic and Applied Microbiology 6(2);183-195.

Steidler06: Steidler L, Rottiers P (2006). "Therapeutic drug delivery by genetically modified Lactococcus lactis." Ann N Y Acad Sci 1072;176-86. PMID: 17057198

Sybesma03: Sybesma W, Starrenburg M, Kleerebezem M, Mierau I, de Vos WM, Hugenholtz J (2003). "Increased production of folate by metabolic engineering of Lactococcus lactis." Appl Environ Microbiol 69(6);3069-76. PMID: 12788700

Sybesma03a: Sybesma W, Van Den Born E, Starrenburg M, Mierau I, Kleerebezem M, De Vos WM, Hugenholtz J (2003). "Controlled modulation of folate polyglutamyl tail length by metabolic engineering of Lactococcus lactis." Appl Environ Microbiol 69(12);7101-7. PMID: 14660354

Sybesma04: Sybesma W, Burgess C, Starrenburg M, van Sinderen D, Hugenholtz J (2004). "Multivitamin production in Lactococcus lactis using metabolic engineering." Metab Eng 6(2);109-15. PMID: 15113564

vanHylckama06: van Hylckama Vlieg JE, Rademaker JL, Bachmann H, Molenaar D, Kelly WJ, Siezen RJ (2006). "Natural diversity and adaptive responses of Lactococcus lactis." Curr Opin Biotechnol 17(2);183-90. PMID: 16517150

Wels19: Wels M, Siezen R, van Hijum S, Kelly WJ, Bachmann H (2019). "Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity." Front Microbiol 10;4. PMID: 30766512

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