Acinetobacter baylyi explained

Acinetobacter baylyi is a bacterial species of the genus Acinetobacter.[1] The species naming designation was given after the discovery of strains in activated sludge in Victoria, Australia, in 2003.[2] A. baylyi is named after the late Dr. Ronald Bayly, an Australian microbiologist who contributed significantly to research on aromatic compound catabolism in diverse bacteria, including strains of Pseudomonas, Alcaligenes, and Acinetobacter.[3] The new species designation in 2003 was found to apply to an already well-studied Acinetobacter strain known as ADP1 (previously known as BD413), a derivative of a soil isolate characterized in 1969.[4] Strain ADP1 was previously designated Acinetobacter sp. and Acinetobacter calcoaceticus. Research, particularly in the field of genetics, has established A. baylyi as a model organism.[5] [6]

As with other species of Acinetobacter, it is a nonmotile, Gram-negative coccobacillus. It grows under strictly aerobic conditions, is catalase-positive, nitrate-negative, oxidase-negative, and non-fermentative.[7] The species is naturally competent, meaning that it can take up free exogenous DNA from its surroundings without being forced, and could then, if there are complementary sequences upstream and downstream the exogenous DNA, potentially incorporate it into its own chromosomal DNA by transformation.[8] Its natural transformation and homologous recombination are exceptionally efficient in comparison to all studied microbes, thus contributing to its experimental utility.

A. baylyi is used for industrial purposes, and has shown promise as a method for alternative fuel sources, monitoring operation and efficiency of machinery impacting the environment, and aiding in cleaning up oil spills.[9]

Metabolism

A. baylyi metabolic pathways have been used for many studies in microbial metabolism, known for its fast growth rate and ability to be easily cultured. A. baylyi can be cultured in media using organic carbon sources to survive such as succinate, pyruvate, acetate, and ethanol.[10] A. baylyi is known as an omnipresent soil bacterium, meaning it can be found in a variety of soils in nature.

A. baylyi prefers to utilize organic carbon sources that can enter the citric acid cycle quickly. A. baylyi is able to utilize aromatic compounds as organic carbon and energy sources through the β-ketoadipate pathway. Aromatic compounds are first transformed into catechol and protocatechuate, which then are transformed into the citric acid cycle substrates succinyl-CoA and acetyl-CoA. Both catechol and protocatechuate can be formed into succinyl-CoA and acetyl-CoA.[11] [12]

A. baylyi's glucose metabolism is slower in comparison to its metabolism of aromatic compounds, as it lacks a gene encoding for pyruvate kinase, a vital enzyme in glycolysis for transforming phosphoenolpyruvate into pyruvate.[13] [14] When glucose is the primary carbon source available, A. baylyi can metabolize glucose by first oxidizing it into gluconate, which feeds into the Entner-Doudoroff pathway. Without pyruvate kinase, A. baylyi has to use a work-around of transforming the phosphoenolpyruvate into oxaloacetate, then malate, which can then become pyruvate and enter the pyruvate dehydrogenase complex and later the citric acid cycle.

Unlike other bacteria that can predominantly use L-amino acids, A. baylyi is an example of metabolic versatility with its ability to utilize D-Asp and L-Asp amino acids as both a primary carbon and nitrogen source, thus opening the door to see how D-enantiomers can be used for bacterial growth.[15]

Experiments have shown that A. baylyi uses intracellular arginine to produce a biodegradable alternative to petroleum-based plastics known as polyaspartic acid. A. baylyi uses arginine to first produce cyanophycin polypeptides, a transient source of nitrogen, which can then be converted to polyaspartic acid.[16] Cyanophycin is predominantly formed when nitrogen sources are low, and said nitrogen is released by cyanophycinase when environmental nitrogen is limited.

Genetics

One major characteristic of A. baylyi is its ability to take in free DNA from the environment. It does so by importing the DNA by natural transformation, a mechanism that incorporates exogenous DNA into its chromosome, characteristic of A. baylyi. The genome of A. baylyi has been completely sequenced, and roughly 35% of A. baylyi's genome sequence is solely devoted for encoding the machinery required for efficient uptake of exogenous DNA into its cell.[17] If there are complementary sequences upstream and downstream of the exogenous DNA, A. baylyi can perform recombination. This mechanism strongly depends on A. baylyi's DNA strand break repair system to ensure success of DNA sequence exchange.[18] Most bacteria struggle to achieve this exchange of adaptive traits from outside DNA via simple point mutations, so the ease at which A. baylyi can take in and incorporate foreign DNA is beneficial to its survival.[19] This also makes A. baylyi an ideal microbe for laboratory experiments. Collections of multiple single-gene mutations, caused by deletions, on dispensable genes of the ADP1 strain have been constructed. With the knowledge of the entire genome sequence and the mutants, scientists are able to know how the ADP1 strain will function in any situation, which expands the capability of the strain for industrial and environmental applications.[20]

A. baylyi can undergo gene duplication and amplification (gda) mutations. Gda mutations are a form of spontaneous mutations that occur where a gene is copied many times and repeated in the genome, but there are many unknowns about the mechanism behind these mutations. A. baylyi has been used by scientists as a model organism for researching gda mutations, one example is its ability to adapt and survive on the substrate benzoate. The catabolism of benzoate yields a metabolite that is toxic at high concentrations in the cell, muconate. For A. baylyi to survive on benzoate, it requires high levels of expression in two genes, catA and catBCIJFD. These genes are amplified to avoid the accumulation of muconate, the toxic intermediate, produced from benzoate metabolism .[21] [22] [23]

The facilitation of A. baylyi's ability in natural transformation, or horizontal gene transfer (HGT) processes, may be aided by the mechanisms of outer membrane vesicles (OMVs). OMVs are produced via vesiculation, the bulging of the outer membrane followed by the constriction and release of small, spherical structures from the bacterium, and are composed of various periplasmic components, including proteins and lipids, as well as some genetic material. OMVs play significant roles in intracellular communication, virulence/bacterial defenses, and adaptation to environmental stress. OMVs released by A. baylyi offer a mode of gene transfer that is not susceptible to degradation by nucleases, contributing to the microbe's high survival rate and antibiotic resistance; however, environmental stress factors can impact the efficiency of these OMVs, ranging from levels of vesicle release to genetic content and HGT abilities.[24]

A. baylyi strains have also been associated with bacterial adhesion and biofilm formation, particularly as a control in comparative experiments with other Acinetobacter species.[25] Biofilms arise from the aggregation of surface microbial cells enveloped within a matrix of extracellular polymeric substances.[26] The biofilms of Acinetobacter species can range in adhesion strength and thickness, and Acinetobacter baumannii is the most commonly associated with various infectious diseases, including cystic fibrosis or urinary tract infections, due to their ability to adhere to medical devices composed of plastic or glass. It has been found that two possible genes may be significant to biofilm formation within the Acinetobacter species: Fimbrial-biogenesis protein (3317) and Putative Surface protein.

ADP1 Strain

A. baylyi, specifically the strain ADP1, has been used for over a quarter of a century in several molecular biology studies due to its strong ability to easily undergo genetic transformation. For these reasons, A. baylyi is used in multiple laboratory techniques as a model organism. These include genetics, specifically gene duplication and amplification as well as bacterial metabolism. The microbe has also been studied for its potential use an alternative triacylglycerol (TAG) source, as under nitrogen limiting conditions it is able to transform excess organic matter into wax esters and triacylglycerols (TAGs) as a lipid storage form through the isoenzymes wax ester synthase/diacylglycerol acyltransferase.[27] The concentration of wax esters and triacylglycerols that the ADP1 strain produces depends on the organic matter present in medium of which the A. baylyi is grown on. Work has been done to genetically modify the metabolism of A. baylyi ADP1 so that it is able to still produce wax esters in a nitrogen-rich environment. This is achieved by overexpressing the gene acr1 and deleting the gene aceA, as this will redirect the movement of carbon in ADP1's metabolism so that it becomes a wax ester.[28]

Applications

A. baylyi is a soil-based microbe, and can be sourced from contaminated environments like diesel oil- and crude oil-contaminated soils, contaminated river waters, activated sludge, lignocellulosic biomass, and more. The microbe is able to live in activated sludge that arise from a variety of pollutants, especially kinds those containing aromatic compounds, heavy metals, and aliphatic substances. A. baylyi has potential use for cleaning up contaminated natural environments via degradation, especially with management and supplementation of other necessary nutrients.[29]

A. baylyi also has the potential as a non-toxic biosurfactant alternative, emulsan, helping to break apart aggregated hydrophobic compounds like oil. Emulsan serves a range of industrial functions from a basic degreaser to emulsification of oil for subsequent removal or aid in transport, as the oil's viscosity is decreased and can move more smoothly through pipes. Additionally, emulsified oil can act as another source of energy. then makes it easier to degrade the compounds and remove them from the environment, ranging from functions.[30]

A. baylyis ability to create TAGs has been used as a potential alternative method of producing TAG-based products like cosmetics, oleochemicals, and biofuels. They are currently made with the TAG sources of vegetable oils, animal fats, and recycled greases. A. baylyi is particularly notable with TAG production as it has low selectivity on what kind of alcohol-based substrate to use.[31]

It has been proposed to combine A. baylyi's abilities to survive in contaminated environments as well as natural transformation in order to use the microbe as a biosensor. By incorporating DNA in A. baylyi ADP1 strain that will generate bioluminescence when activated by pollutant degradation mechanisms, the monitoring of soils and water supplies would be elevated.[32]

One of the most abundant resources is lignin, a complex organic polymer in plants responsible for reinforcing the rigidity of the cell wall and making them "woody."[33] This is typically discarded during industrial processes as it is difficult to breakdown the lignin into something usable.[34] Similar to creating an A. baylyi mutant strain specifically for monitoring of cleanliness of soils and waterways, incorporating DNA in A. baylyi ADP1 would result in a further optimized ability to degrade difficult compounds like lignin and make it into a useable molecule, like lipids.[35] This will lead to more efficient use of lignin-containing plants like trees as well as provide an alternative fuel source to petroleum-based products.

Notes and References

  1. Web site: Genus: Acinetobacter . lpsn.dsmz.de.
  2. Carr . Emma L. . Kämpfer . Peter . Patel . Bharat K. C. . Gürtler . Volker . Seviour . Robert J. . April 9, 2003 . Seven novel species of Acinetobacter isolated from activated sludge . International Journal of Systematic and Evolutionary Microbiology . 53 . 4 . 953–963 . 10.1099/ijs.0.02486-0 . 12892111 . free.
  3. Web site: 2021-07-07 . VALE Dr. Ronald Cecil Bayly . 2024-03-18 . Monash Biomedicine Discovery Institute . en.
  4. Vaneechoutte . Mario . Young . David M. . Ornston . L. Nicholas . De Baere . Thierry . Nemec . Alexandr . Van Der Reijden . Tanny . Carr . Emma . Tjernberg . Ingela . Dijkshoorn . Lenie . January 2006 . Naturally Transformable Acinetobacter sp. Strain ADP1 Belongs to the Newly Described Species Acinetobacter baylyi . Applied and Environmental Microbiology . en . 72 . 1 . 932–936 . 2006ApEnM..72..932V . 10.1128/AEM.72.1.932-936.2006 . 0099-2240 . 1352221 . 16391138.
  5. Juni . Elliot . November 1972 . Interspecies Transformation of Acinetobacter : Genetic Evidence for a Ubiquitous Genus . Journal of Bacteriology . en . 112 . 2 . 917–931 . 10.1128/jb.112.2.917-931.1972 . 4563985 . 251504 . 0021-9193.
  6. Young . David M. . Parke . Donna . Ornston . L. Nicholas . 2005-10-01 . Opportunities for Genetic Investigation Afforded by Acinetobacter baylyi, A Nutritionally Versatile Bacterial Species That Is Highly Competent for Natural Transformation . Annual Review of Microbiology . 59 . 1 . 519–551 . 10.1146/annurev.micro.59.051905.105823 . 16153178 . 0066-4227.
  7. Web site: 2020-02-01 . Acinetobacter baylyi Biofilm Formation Dependent Genes . 2024-02-15 . Journal of Pure and Applied Microbiology . en-US.
  8. Acinetobacter baylyi ADP1: Transforming the choice of model organism. Kathryn T.. Elliott. Ellen L.. Neidle. April 9, 2011. IUBMB Life. 63. 12. 1075–1080. 10.1002/iub.530. 22034222. free.
  9. Santala . Suvi . Efimova . Elena . Kivinen . Virpi . Larjo . Antti . Aho . Tommi . Karp . Matti . Santala . Ville . 2011 . Improved Triacylglycerol Production in Acinetobacter baylyi ADP1 by Metabolic Engineering . Microbial Cell Factories . en . 10 . 1 . 36 . 10.1186/1475-2859-10-36 . 1475-2859 . 3112387 . 21592360 . free.
  10. Salcedo-Vite . Karina . Sigala . Juan-Carlos . Segura . Daniel . Gosset . Guillermo . Martinez . Alfredo . 2019-08-01 . Acinetobacter baylyi ADP1 growth performance and lipid accumulation on different carbon sources . Applied Microbiology and Biotechnology . en . 103 . 15 . 6217–6229 . 10.1007/s00253-019-09910-z . 31144015 . 0175-7598.
  11. Stuani . Lucille . Lechaplais . Christophe . Salminen . Aaro V. . Ségurens . Béatrice . Durot . Maxime . Castelli . Vanina . Pinet . Agnès . Labadie . Karine . Cruveiller . Stéphane . Weissenbach . Jean . de Berardinis . Véronique . Salanoubat . Marcel . Perret . Alain . December 2014 . Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach . Metabolomics . en . 10 . 6 . 1223–1238 . 10.1007/s11306-014-0662-x . 1573-3882 . 4213383 . 25374488.
  12. Book: Williams . Peter A. . Acinetobacter molecular microbiology . Kay . Catherine M. . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 99 . EN . 154685348.
  13. Kannisto . Matti . Aho . Tommi . Karp . Matti . Santala . Ville . 2014-11-15 . Liu . S.-J. . Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose . Applied and Environmental Microbiology . en . 80 . 22 . 7021–7027 . 2014ApEnM..80.7021K . 10.1128/AEM.01837-14 . 0099-2240 . 4249021 . 25192990.
  14. Calil Brondani . Juliana . Afful . Derrick . Nune . Hanna . Hart . Jesse . Cook . Shelby . Momany . Cory . June 2023 . Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme . Protein Expression and Purification . en . 206 . 106254 . 10.1016/j.pep.2023.106254 . 36804950.
  15. Bedore . Stacy R. . Schmidt . Alicia L. . Slarks . Lauren E. . Duscent-Maitland . Chantel V. . Elliott . Kathryn T. . Andresen . Silke . Costa . Flavia G. . Weerth . R. Sophia . Tumen-Velasquez . Melissa P. . Nilsen . Lindsey N. . Dean . Cassandra E. . Karls . Anna C. . Hoover . Timothy R. . Neidle . Ellen L. . 2022-08-09 . Alexandre . Gladys . Regulation of l - and d -Aspartate Transport and Metabolism in Acinetobacter baylyi ADP1 . Applied and Environmental Microbiology . en . 88 . 15 . e0088322 . 10.1128/aem.00883-22 . 0099-2240 . 9361831 . 35862682. 2022ApEnM..88E.883B .
  16. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 252 . 154685348.
  17. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 232 . 154685348.
  18. Hülter . Nils . Sørum . Vidar . Borch-Pedersen . Kristina . Liljegren . Mikkel M. . Utnes . Ane L. G. . Primicerio . Raul . Harms . Klaus . Johnsen . Pål J. . 2017-02-15 . Costs and benefits of natural transformation in Acinetobacter baylyi . BMC Microbiology . en . 17 . 1 . 34 . 10.1186/s12866-017-0953-2 . free . 1471-2180 . 5312590 . 28202049.
  19. Utnes . Ane L G . Sørum . Vidar . Hülter . Nils . Primicerio . Raul . Hegstad . Joachim . Kloos . Julia . Nielsen . Kaare M . Johnsen . Pål J . 2015-10-01 . Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi . The ISME Journal . en . 9 . 10 . 2221–2231 . 10.1038/ismej.2015.35 . 25848876 . 4579475 . 2015ISMEJ...9.2221U . 1751-7362.
  20. de Berardinis . Véronique . Vallenet . David . Castelli . Vanina . Besnard . Marielle . Pinet . Agnès . Cruaud . Corinne . Samair . Sumitta . Lechaplais . Christophe . Gyapay . Gabor . Richez . Céline . Durot . Maxime . Kreimeyer . Annett . Le Fèvre . François . Schächter . Vincent . Pezo . Valérie . 2008 . A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1 . Molecular Systems Biology . 4 . 174 . 10.1038/msb.2008.10 . 1744-4292 . 2290942 . 18319726.
  21. Reams . Andrew B . Neidle . Ellen L . Gene amplification involves site-specific short homology-independent illegitimate recombination in Acinetobacter sp. strain ADP1 . Journal of Molecular Biology . 7 May 2004 . 338 . 4 . 643–656 . 10.1016/j.jmb.2004.03.031 . 15099734 .
  22. Seaton . Sarah C . Elliott . Kathryn T . Cuff . Laura E . Laniohan . Nicole S . Patel . Poonam R . Niedle . Ellen L . Genome-wide selection for increased copy number in Acinetobacter baylyi ADP1: locus and context-dependent variation in gene amplification . Molecular Microbiology . 29 December 2011 . 83 . 3 . 520–535 . 10.1111/j.1365-2958.2011.07945.x . 22211470 .
  23. Ezezika . Obidimma C. . Collier-Hyams . Lauren S. . Dale . Haley A. . Burk . Andrew C. . Neidle . Ellen L. . March 2006 . CatM Regulation of the benABCDE Operon: Functional Divergence of Two LysR-Type Paralogs in Acinetobacter baylyi ADP1 . Applied and Environmental Microbiology . 72 . 3 . 1749–1758 . 10.1128/aem.72.3.1749-1758.2006 . 16517618 . 0099-2240. 1393229 . 2006ApEnM..72.1749E .
  24. Fulsundar . Shweta . Harms . Klaus . Flaten . Gøril E. . Johnsen . Pål J. . Chopade . Balu Ananda . Nielsen . Kaare M. . June 2014 . Kivisaar . M. . Gene Transfer Potential of Outer Membrane Vesicles of Acinetobacter baylyi and Effects of Stress on Vesiculation . Applied and Environmental Microbiology . en . 80 . 11 . 3469–3483 . 10.1128/AEM.04248-13 . 0099-2240 . 4018862 . 24657872. 2014ApEnM..80.3469F .
  25. Vallenet . David . Nordmann . Patrice . Barbe . Valérie . Poirel . Laurent . Mangenot . Sophie . Bataille . Elodie . Dossat . Carole . Gas . Shahinaz . Kreimeyer . Annett . Lenoble . Patricia . Oztas . Sophie . Poulain . Julie . Segurens . Béatrice . Robert . Catherine . Abergel . Chantal . 2008-03-19 . Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles . PLOS ONE . en . 3 . 3 . e1805 . 2008PLoSO...3.1805V . 10.1371/journal.pone.0001805 . 1932-6203 . 2265553 . 18350144 . free.
  26. Lopez . D. . Vlamakis . H. . Kolter . R. . 2010-07-01 . Biofilms . Cold Spring Harbor Perspectives in Biology . en . 2 . 7 . a000398 . 10.1101/cshperspect.a000398 . 1943-0264 . 2890205 . 20519345.
  27. Kalscheuer . Rainer . Steinbüchel . Alexander . March 2003 . A Novel Bifunctional Wax Ester Synthase/Acyl-CoA:Diacylglycerol Acyltransferase Mediates Wax Ester and Triacylglycerol Biosynthesis inAcinetobacter calcoaceticus ADP1 . Journal of Biological Chemistry . en . 278 . 10 . 8075–8082 . 10.1074/jbc.M210533200 . 12502715 . free.
  28. Luo . Jin . Efimova . Elena . Losoi . Pauli . Santala . Ville . Santala . Suvi . June 2020 . Wax ester production in nitrogen-rich conditions by metabolically engineered Acinetobacter baylyi ADP1 . Metabolic Engineering Communications . en . 10 . e00128 . 10.1016/j.mec.2020.e00128 . 7251950 . 32477866.
  29. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 239–240 . 154685348.
  30. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 241, 249 . 154685348.
  31. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 250–251 . 154685348.
  32. Book: Gutnick . David L. . Acinetobacter molecular microbiology . Bach . Horacio . 2008 . Caister Academic Press . 978-1-904455-20-2 . Gerischer . Ulrike . Norfolk, UK . 253 . 154685348.
  33. Book: Kirk-Othmer Encyclopedia of Chemical Technology . 2001-01-26 . Wiley . 978-0-471-48494-3 . Kirk-Othmer . 1 . en . 10.1002/0471238961.12090714120914.a01.pub2.
  34. Luo . Jin . Lehtinen . Tapio . Efimova . Elena . Santala . Ville . Santala . Suvi . 2019-03-11 . Synthetic metabolic pathway for the production of 1-alkenes from lignin-derived molecules . Microbial Cell Factories . 18 . 1 . 48 . 10.1186/s12934-019-1097-x . free . 1475-2859 . 6410514 . 30857542.
  35. Luo . Jin Jr . November 2016 . Examined by Ville Santala and Dr. Suvi Santala . Intracellular Lipid Production from Lignin Model Monomers by Acinetobacter baylyi ADP1 . Master of Science Thesis . en.

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