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    Acinetobacter baylyi

    From Wikipedia - Reading time: 15 min
    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 characterization of strains isolated from 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] For a long time, the taxonomy of Acinetobacter species was complicated by the lack of distinguishing traits. Strain ADP1 was long classified as Acinetobacter calcoaceticus and it was later referred to without a species name (Acinetobacter sp.) Research, particularly in the field of genetics and aromatic compound catabolism, established A. baylyi as a model organism.[3][4]

    Acinetobacter baylyi 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 exogenous DNA from its surroundings. If there is sufficient sequence identity between the transforming DNA and the genome of the recipient, the foreign DNA will be integrated in the chromosome by allelic replacement.[7] The processes of natural transformation and homologous recombination are incredibly efficient in A. baylyi compared to all studied microbes, thus contributing to its experimental utility.[8] There are numerous biotechnology applications for A. baylyi, such as producing alternative fuel sources and chemicals, acting as a host for biosensors to monitor the presence of important compounds, and aiding in degradation of pollutants.[9][10][11]

    Genetics

    [edit]

    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.[12] The genome of A. baylyi has been completely sequenced, and roughly 35% of A. baylyi's genome sequence encodes proteins that contribute to transformation and recombination .[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 is an evolutionary mechanism beneficial for survival. [15] This also makes A. baylyi an ideal microbe for laboratory experiments.[12] Multiple single-gene deletion mutations on dispensable genes of the ADP1 strain have been collected. 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]

    Specifically, the strain ADP1 of A. baylyi, 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[12]. For these reasons, A. baylyi is used in multiple laboratory techniques as a model organism, particularly in genetics research. This includes studying gene duplication and amplification, as well as exploring bacterial metabolism. Work has been done to genetically modify the metabolism of A. baylyi ADP1, such as overexpressing the gene acr1 and deleting the gene aceA to alter carbon flow. These modifications enable the strain to produce wax esters even in a nitrogen-rich environment.

    A. baylyi's ability to use natural transformation, or horizontal gene transfer (HGT), 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.[23]

    Metabolism

    [edit]

    A. baylyi has been used to study many biochemical pathways, since it is metabolically versatile, it grows rapidly, and is easily cultured. [12] A. baylyi can be cultured in media containing diverse carbon sources such as succinate, pyruvate, acetate, ethanol, and many aromatic compounds.[24] A. baylyi is omnipresent in nature and is found in a wide variety of terrestrial and aqueous environments. [1] Organic growth substrates are oxidized to compounds that can enter the citric acid cycle, also known as the tricarboxylic acid (TCA) cycle, quickly. Aromatic compounds are catabolized through the β-ketoadipate pathway, a pathway by which many different aromatic compounds are converted into either catechol or protocatechuate, which serve as substrates for a aromatic ring-opening dioxygenase. Parallel multi-step pathways yield succinyl-CoA and acetyl-CoA after the ring cleavage of catechol or protocatechuate. .[25][26]

    A. baylyi has an atypical pathway for glucose metabolism, also known as glycolysis, as it lacks a sugar phosphotransferase system (PTS) for glucose uptake and phosphorylation, and pyruvate kinase, a vital enzyme in glycolysis that produces pyruvate from phosphoenolpyruvate .[25][27][24][28] When glucose is readily available, A. baylyi can metabolize glucose by first oxidizing it into gluconate, which then enters the Entner-Doudoroff pathway. Without pyruvate kinase, A. baylyi can produces pyruvate from the cleavage of 2-keto-3-deoxy-6-phosphogluconate. Additional pyruvate is produced from the enzymatic conversion of phosphoenolpyruvate to oxalacetate, then malate, and then pyruvate. [27]

    Unlike other bacteria that can predominantly use L-amino acids, A. baylyi is able to utilize D-aspartate as well as L-aspartate amino acids as both a primary carbon and nitrogen source, thus leading scientists to study how D-enantiomers can be used for bacterial growth.[29] 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.[12][30] Cyanophycin is predominantly formed when nitrogen sources are low, and nitrogen is released by cyanophycinase when environmental nitrogen is limited.[30]

    Applications

    [edit]

    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 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.[31]

    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 oil emulsion 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.[32]

    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.[33] A. baylyi is particularly notable with TAG production as it has low selectivity on what kind of alcohol-based substrate to use.[34]

    It has been proposed to combine A. baylyi's abilities to survive in contaminated environments and to undergo 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.[35]

    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."[36] This is typically discarded during industrial processes as it is difficult to breakdown the lignin into something usable.[37] By repressing a gene encoding for catabolite repression, A. baylyi ADP1 has a greater ability to degrade lignin into useable wax esters.[38] 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.[37]

    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 TAGs as a lipid storage form through the isoenzymes wax ester synthase/diacylglycerol acyltransferase.[39][24] 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.[24] 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.[40]

    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.[41]

    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.[41]

    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.[41]

    References

    [edit]
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    [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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