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Acinetobacter baylyi

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A. baylyi under 10x ocular lens and 100x objective lens with crystal violet stain.

Acinetobacter baylyi
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Gammaproteobacteria
Order: Pseudomonadales
Family: Moraxellaceae
Genus: Acinetobacter
Species:
A. baylyi
Binomial name
Acinetobacter baylyi
Carr et al. 2003

Acinetobacter baylyi is a bacterial species of the genus Acinetobacter. The species designation was given after the discovery of strains in activated sludge in Victoria, Australia, in 2003.[1] 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. 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.[2] 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.[3][4]

Acinetobacter is a nonmotile, Gram-negative coccobacillus. It grows under strictly aerobic conditions, is catalase-positive, nitrate-negative, oxidase-negative, and non-fermentative.[5] [6]The species is naturally competent, meaning the bacteria can take up free exogenous DNA from its surroundings. If there are complementary sequences upstream and downstream the exogenous DNA, A. baylyi can incorporate the foreign DNA into its own genome by transformation.[7] Its natural transformation and homologous recombination are exceptionally efficient in comparison to all studied microbes, thus contributing to its experimental utility.[8]

A. baylyi is used for industrial purposes, such as alternative fuel sources, monitoring operation and efficiency of machinery, and aiding in cleaning up oil spills.[9][10][11][12]

Genetics

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One major characteristic of A. baylyi is its ability to take in free DNA from the environment by natural transformation, a mechanism that incorporates exogenous DNA into its genome.[7] 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.[13] 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.[14] The unique capability of A. baylyi to take in DNA from the environment possess as an evolutionary mechanism that is beneficial for survival. [15] This also makes A. baylyi an ideal microbe for laboratory experiments.[7] 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.[16]

A. baylyi can undergo gene duplication and amplification (GDA) mutations. GDA mutations are a form of spontaneous mutations that result in a gene reoccurring in the genome, but little is understood about the mechanism behind these mutations. A. baylyi has been used by scientists as a model organism for researching GDA mutations. One reason is its ability to adapt and survive on the substrate benzoate. The catabolism of benzoate yields a product, muconate, that is toxic at high concentrations in the cell. For A. baylyi to survive on benzoate, it expresses two genes, catA and catBCIJFD, which aid in the breakdown on muconate. [17][18][19]

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.[20]

A. baylyi strains have also been associated with bacterial adhesion and biofilm formation, particularly as a control in comparative experiments with other Acinetobacter species.[21] Biofilms arise from the aggregation of surface microbial cells enveloped within a matrix of extracellular polymeric substances.[22] 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 and putative surface protein.[5]

ADP1 Strain

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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.[7][23] 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.[7][24] 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.[25][26] 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.[26] 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.[27]

Metabolism

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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.[7] A. baylyi can be cultured in media using organic carbon sources to survive such as succinate, pyruvate, acetate, and ethanol.[26]

A. baylyi primarily utilizes organic carbon sources and enters 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 or protocatechuate, which then are transformed into the substrates succinyl-CoA and acetyl-CoA. Both catechol and protocatechuate can be formed into succinyl-CoA and acetyl-CoA.[28][29]

A. baylyi has an atypical pathway for glucose metabolism as it lacks a gene encoding for pyruvate kinase, a vital enzyme in glycolysis for transforming phosphoenolpyruvate into pyruvate.[28][23][26][24] 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.[23]

Unlike other bacteria that can predominantly use L-amino acids, A. baylyi is able 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.[30]

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.[7][31] Cyanophycin is predominantly formed when nitrogen sources are low, and said nitrogen is released by cyanophycinase when environmental nitrogen is limited.[31]

Applications

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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.[32]

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.[12]

A. baylyi's 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.[9] A. baylyi is particularly notable with TAG production as it has low selectivity on what kind of alcohol-based substrate to use.[33]

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.[11]

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."[34] This is typically discarded during industrial processes as it is difficult to breakdown the lignin into something usable.[10] 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.[10]

In 2022, a study using Acinetobacter baylyi, specifically the BD413 strain, focused on antibiotic resistance genes in microbes found on lettuce leaves. Although A. baylyi is known to be non-pathogenic, its ability to take up and integrate antibiotic resistance genes is of significant interest. The researchers aimed to explore how this bacterium acquires resistance genes through natural transformation, a process where bacteria uptake and incorporate free DNA from their surroundings.[36]

The experiment involved introducing A. baylyi BD413 onto the surface of lettuce leaves alongside bacteria carrying a plasmid with a specific antibiotic resistance gene. They discovered that A. baylyi could successfully absorb and integrate the antibiotic resistance gene into its genome through homologous recombination, thus acquiring resistance. The study also found that A. baylyi could penetrate the lettuce's internal tissues, indicating that the bacterium can carry antibiotic resistance genes into the plant’s endosphere. This suggests that A. baylyi not only acquires antibiotic resistance genes on the plant surface but could also transport these genes into the plant itself.[36]

These findings highlight the value of A. baylyi as a useful tool for studying gene transfer processes in non-pathogenic bacteria on plants. While the experiment highlights its role in understanding the spread of antibiotic resistance genes within agricultural environments, it may prove to be an important subject for future research aimed at controlling antibiotic resistance in other settings, such as a clinical setting.[36]

References

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  23. ^ a b c Kannisto, Matti; Aho, Tommi; Karp, Matti; Santala, Ville (2014-11-15). Liu, S.-J. (ed.). "Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose". Applied and Environmental Microbiology. 80 (22): 7021–7027. Bibcode:2014ApEnM..80.7021K. doi:10.1128/AEM.01837-14. ISSN 0099-2240. PMC 4249021. PMID 25192990.
  24. ^ a b 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. 206: 106254. doi:10.1016/j.pep.2023.106254. PMID 36804950.
  25. ^ 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. 278 (10): 8075–8082. doi:10.1074/jbc.M210533200. PMID 12502715.
  26. ^ a b c d 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. 103 (15): 6217–6229. doi:10.1007/s00253-019-09910-z. ISSN 0175-7598. PMID 31144015.
  27. ^ 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. 10: e00128. doi:10.1016/j.mec.2020.e00128. PMC 7251950. PMID 32477866.
  28. ^ a b 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. 10 (6): 1223–1238. doi:10.1007/s11306-014-0662-x. ISSN 1573-3882. PMC 4213383. PMID 25374488.
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  36. ^ a b c Riva V, Patania G, Riva F, Vergani L, Crotti E, Mapelli F (September 2022). "Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere". Antibiotics. 11 (9): 1231. doi:10.3390/antibiotics11091231. PMC 9495178. PMID 36140010.

[1]

  1. ^ Riva, Valentina; Patania, Giovanni; Riva, Francesco; Vergani, Lorenzo; Crotti, Elena; Mapelli, Francesca (2022-09-10). "Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere". Antibiotics. 11 (9): 1231. doi:10.3390/antibiotics11091231. ISSN 2079-6382. PMC 9495178. PMID 36140010.
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