Database Authors
Anamika Kothari1, Suzanne Paley1, Ron Caspi1, Anahit Penesyan2, Brendan Wilson-Mortier2, Amanda Mackie2, Ian Paulsen2, Peter D Karp1
1SRI International, 2Macquarie University
Summary Cupriavidus necator is a Gram-negative, rod-shaped bacterium belonging to the class Betaproteobacteria. This organism has undergone several taxonomic reclassifications, and has been previously known as Alcaligenes eutrophus, Ralstonia eutropha, and Wautersia eutropha [Vandamme04].

C. necator exhibits remarkable metabolic flexibility, enabling it to thrive in diverse environmental conditions [Schwartz03, Pohlmann06, Jahn24]. The metabolic versatility has made C. necator a promising chassis organism for various biotechnological applications [Pearcy22].

C. necator can grow as a lithoautotroph by oxidizing hydrogen (H2) as an energy source, a characteristic that classifies it among "knallgas" bacteria [Schlegel61] (bacteria that are able to fix carbon dioxide using H2 as their chemical energy source). This bacterium can also adapt to heterotrophic growth, utilizing various organic compounds [Pohlmann06]. Under anaerobic conditions, C. necator performs denitrification, reducing nitrate or nitrite to nitrogen gas [Cramm99, Cramm97, Pohlmann00]. The organism can also fix carbon dioxide via the Calvin-Benson-Bassham cycle [Bowien02].

A notable feature of C. necator is its ability to synthesize and accumulate large quantities of polyhydroxyalkanoates (PHAs), particularly polyhydroxybutyrate (PHB), as intracellular carbon and energy reserves [Madison99, KutralamMuniasa18].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 28.5 and MetaCyc [Caspi18] version 28.5 on 23-Sep-2024.

We thank Christopher Johnson, Emm Fulk, Chris Calvey, and Jessica Roberts (National Renewable Energy Laboratory, US), as well as Paige Erpf (Macquarie University, Australia), for their assistance in identifying recent advancements in C. necator research and for their critical review of the C. necator H16 draft database.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 13,7463,67769824,049,965NCBI Assembly:GCF_004798725.1
Chromosome 22,5782,56612392,912,457NCBI Assembly:GCF_004798725.1
pHG1393392151452,139NCBI Assembly:GCF_004798725.1
Total:6,8896,635821727,414,561
Ortholog data available?Yes
Database Contents
Genes6,717
Pathways383
Enzymatic Reactions1,978
Transport Reactions60
Polypeptides6,636
Protein Complexes248
Enzymes1,383
Transporters723
Compounds1,695
Transcription Units4,958
tRNAs63
Growth Media6
Transcriptional Regulation3
Protein Features23,167
GO Annotations38,284
Gene Essentiality Datasets2
Database Version29.6
Synonyms Cupriavidus necator H16
Alcaligenes eutrophus H16
Ralstonia eutropha H16
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Betaproteobacteria
Burkholderiales
Burkholderiaceae
Cupriavidus
Cupriavidus necator
Cupriavidus necator H16
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11372030
NCBI BioProjectPRJNA224116
NCBI-Taxonomy381666
Environmentsludge
Geographic LocationGermany
Collection Date1975-01-29/1975-02-26
Annotation ProviderNCBI RefSeq
Annotation Date2024-03-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Bowien02: Bowien B, Kusian B (2002). "Genetics and control of CO(2) assimilation in the chemoautotroph Ralstonia eutropha." Arch Microbiol 178(2);85-93. PMID: 12115053

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

Cramm97: Cramm R, Siddiqui RA, Friedrich B (1997). "Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16." J Bacteriol 179(21);6769-77. PMID: 9352929

Cramm99: Cramm R, Pohlmann A, Friedrich B (1999). "Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16." FEBS Lett 460(1);6-10. PMID: 10571051

Jahn24: Jahn M, Crang N, Gynna AH, Kabova D, Frielingsdorf S, Lenz O, Charpentier E, Hudson EP (2024). "The energy metabolism of Cupriavidus necator in different trophic conditions." Appl Environ Microbiol 90(10);e0074824. PMID: 39320125

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

KutralamMuniasa18: Kutralam-Muniasamy G, Perez-Guevara F (2018). "Genome characteristics dictate poly-R-(3)-hydroxyalkanoate production in Cupriavidus necator H16." World J Microbiol Biotechnol 34(6);79. PMID: 29799066

Madison99: Madison LL, Huisman GW (1999). "Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic." Microbiol Mol Biol Rev 63(1);21-53. PMID: 10066830

Pearcy22: Pearcy N, Garavaglia M, Millat T, Gilbert JP, Song Y, Hartman H, Woods C, Tomi-Andrino C, Reddy Bommareddy R, Cho BK, Fell DA, Poolman M, King JR, Winzer K, Twycross J, Minton NP (2022). "A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications." PLoS Comput Biol 18(5);e1010106. PMID: 35604933

Pohlmann00: Pohlmann A, Cramm R, Schmelz K, Friedrich B (2000). "A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha." Mol Microbiol 38(3);626-38. PMID: 11069685

Pohlmann06: Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Potter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbuchel A, Friedrich B, Bowien B (2006). "Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16." Nat Biotechnol 24(10);1257-62. PMID: 16964242

Schlegel61: Schlegel HG, Goffschalk G, Von Bartha R (1961). "Formation and utilization of poly-beta-hydroxybutyric acid by Knallgas bacteria (Hydrogenomonas)." Nature 191;463-5. PMID: 13747776

Schwartz03: Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G (2003). "Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis." J Mol Biol 332(2);369-83. PMID: 12948488

Vandamme04: Vandamme P, Coenye T (2004). "Taxonomy of the genus Cupriavidus: a tale of lost and found." Int J Syst Evol Microbiol 54(Pt 6);2285-2289. PMID: 15545472

References

Jia01: Jia Y, Yuan W, Wodzinska J, Park C, Sinskey AJ, Stubbe J (2001). "Mechanistic studies on class I polyhydroxybutyrate (PHB) synthase from Ralstonia eutropha: class I and III synthases share a similar catalytic mechanism." Biochemistry 40(4);1011-9. PMID: 11170423


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