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Статті в журналах з теми "Bacterial genetics"

Автор: Grafiati

Опубліковано: 4 червня 2021

Оновлено: 1 серпня 2024

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1

Dionisio, Francisco, Ivan Matic, Miroslav Radman, Olivia R. Rodrigues, and François Taddei. "Plasmids Spread Very Fast in Heterogeneous Bacterial Communities." Genetics 162, no. 4 (December 1, 2002): 1525–32. http://dx.doi.org/10.1093/genetics/162.4.1525.

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Abstract Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This “amplification effect” could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes.

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2

Vollmer, Amy Cheng. "Bacterial Genetics." Developmental Cell 6, no. 5 (May 2004): 617–19. http://dx.doi.org/10.1016/s1534-5807(04)00136-4.

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3

Breeuwer, J. A., and J. H. Werren. "Cytoplasmic incompatibility and bacterial density in Nasonia vitripennis." Genetics 135, no. 2 (October 1, 1993): 565–74. http://dx.doi.org/10.1093/genetics/135.2.565.

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Abstract Cytoplasmically (maternally) inherited bacteria that cause reproductive incompatibility between strains are widespread among insects. In the parasitoid wasp Nasonia, incompatibility results in improper condensation and fragmentation of the paternal chromosomes in fertilized eggs. Some form of genome imprinting may be involved. Because of haplodiploidy, incompatibility results in conversion of (diploid) female eggs into (haploid) males. Experiments show that bacterial density is correlated with compatibility differences between male and female Nasonia. Males from strains with high bacterial numbers are incompatible with females from strains with lower numbers. Temporal changes in compatibility of females after tetracycline treatment are generally correlated with decreases in bacterial levels in eggs. However, complete loss of bacteria in mature eggs precedes conversion of eggs to the "asymbiont" compatibility type by 3-4 days. This result is consistent with a critical "imprinting" period during egg maturation, when cytoplasmic bacteria determine compatibility. Consequent inheritance of reduced bacterial numbers in F1 progeny has different effects on compatibility type of subsequent male vs. female progeny. In some cases, partial incompatibility occurs which results in reduced offspring numbers, apparently due to incomplete paternal chromosome elimination resulting in aneuploidy.

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4

Kussell, Edo, Roy Kishony, Nathalie Q. Balaban, and Stanislas Leibler. "Bacterial Persistence." Genetics 169, no. 4 (January 31, 2005): 1807–14. http://dx.doi.org/10.1534/genetics.104.035352.

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5

Macario, Alberto J. L., and Everly Conway de Macario. "The Archaeal Molecular Chaperone Machine: Peculiarities and Paradoxes." Genetics 152, no. 4 (August 1, 1999): 1277–83. http://dx.doi.org/10.1093/genetics/152.4.1277.

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Abstract A major finding within the field of archaea and molecular chaperones has been the demonstration that, while some species have the stress (heat-shock) gene hsp70(dnaK), others do not. This gene encodes Hsp70(DnaK), an essential molecular chaperone in bacteria and eukaryotes. Due to the physiological importance and the high degree of conservation of this protein, its absence in archaeal organisms has raised intriguing questions pertaining to the evolution of the chaperone machine as a whole and that of its components in particular, namely, Hsp70(DnaK), Hsp40(DnaJ), and GrpE. Another archaeal paradox is that the proteins coded by these genes are very similar to bacterial homologs, as if the genes had been received via lateral transfer from bacteria, whereas the upstream flanking regions have no bacterial markers, but instead have typical archaeal promoters, which are like those of eukaryotes. Furthermore, the chaperonin system in all archaea studied to the present, including those that possess a bacterial-like chaperone machine, is similar to that of the eukaryotic-cell cytosol. Thus, two chaperoning systems that are designed to interact with a compatible partner, e.g., the bacterial chaperone machine physiologically interacts with the bacterial but not with the eucaryal chaperonins, coexist in archaeal cells in spite of their apparent functional incompatibility. It is difficult to understand how these hybrid characteristics of the archaeal chaperoning system became established and work, if one bears in mind the classical ideas learned from studying bacteria and eukaryotes. No doubt, archaea are intriguing organisms that offer an opportunity to find novel molecules and mechanisms that will, most likely, enhance our understanding of the stress response and the protein folding and refolding processes in the three phylogenetic domains.

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6

Bergstrom, Carl T., Marc Lipsitch, and Bruce R. Levin. "Natural Selection, Infectious Transfer and the Existence Conditions for Bacterial Plasmids." Genetics 155, no. 4 (August 1, 2000): 1505–19. http://dx.doi.org/10.1093/genetics/155.4.1505.

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Abstract Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this article, we address the question of how plasmids manage to persist over evolutionary time. Empirical studies suggest that plasmids are not infectiously transmitted at a rate high enough to be maintained as genetic parasites. In part i, we present a general mathematical proof that if this is the case, then plasmids will not be able to persist indefinitely solely by carrying genes that are beneficial or sometimes beneficial to their host bacteria. Instead, such genes should, in the long run, be incorporated into the bacterial chromosome. If the mobility of host-adaptive genes imposes a cost, that mobility will eventually be lost. In part ii, we illustrate a pair of mechanisms by which plasmids can be maintained indefinitely even when their rates of transmission are too low for them to be genetic parasites. First, plasmids may persist because they can transfer locally adapted genes to newly arriving strains bearing evolutionary innovations, and thereby preserve the local adaptations in the face of background selective sweeps. Second, plasmids may persist because of their ability to shuttle intermittently favored genes back and forth between various (noncompeting) bacterial strains, ecotypes, or even species.

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7

Lawrence, J. G., H. Ochman, and D. L. Hartl. "The evolution of insertion sequences within enteric bacteria." Genetics 131, no. 1 (May 1, 1992): 9–20. http://dx.doi.org/10.1093/genetics/131.1.9.

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Abstract To identify mechanisms that influence the evolution of bacterial transposons, DNA sequence variation was evaluated among homologs of insertion sequences IS1, IS3 and IS30 from natural strains of Escherichia coli and related enteric bacteria. The nucleotide sequences within each class of IS were highly conserved among E. coli strains, over 99.7% similar to a consensus sequence. When compared to the range of nucleotide divergence among chromosomal genes, these data indicate high turnover and rapid movement of the transposons among clonal lineages of E. coli. In addition, length polymorphism among IS appears to be far less frequent than in eukaryotic transposons, indicating that nonfunctional elements comprise a smaller fraction of bacterial transposon populations than found in eukaryotes. IS present in other species of enteric bacteria are substantially divergent from E. coli elements, indicating that IS are mobilized among bacterial species at a reduced rate. However, homologs of IS1 and IS3 from diverse species provide evidence that recombination events and horizontal transfer of IS among species have both played major roles in the evolution of these elements. IS3 elements from E. coli and Shigella show multiple, nested, intragenic recombinations with a distantly related transposon, and IS1 homologs from diverse taxa reveal a mosaic structure indicative of multiple recombination and horizontal transfer events.

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8

Townsend, Jeffrey P., Kaare M. Nielsen, Daniel S. Fisher, and Daniel L. Hartl. "Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes." Genetics 164, no. 1 (May 1, 2003): 13–21. http://dx.doi.org/10.1093/genetics/164.1.13.

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Abstract We examine the potential beneficial effects of the expanded access to environmental DNA offered by mutators on the adaptive potential of bacterial populations. Using parameters from published studies of recombination in E. coli, we find that the presence of mutators has the potential to greatly enhance bacterial population adaptation when compared to populations without mutators. In one specific example, for which three specific amino acid substitutions are required for adaptation to occur in a 300-amino-acid protein, we found a 3500-fold increase in the rate of adaptation. The probability of a beneficial acquisition decreased if more amino acid changes, or integration of longer DNA fragments, were required for adaptation. The model also predicts that mutators are more likely than nonmutator phenotypes to acquire genetic variability from a more diverged set of donor bacteria. Bacterial populations harboring mutators in a sequence heterogeneous environment are predicted to acquire most of their DNA conferring adaptation in the range of 13–30% divergence, whereas nonmutator phenotypes become adapted after recombining with more homogeneous sequences of 7–21% divergence. We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to ∼30% divergence.

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9

Dahlberg, Cecilia, and Lin Chao. "Amelioration of the Cost of Conjugative Plasmid Carriage in Eschericha coli K12." Genetics 165, no. 4 (December 1, 2003): 1641–49. http://dx.doi.org/10.1093/genetics/165.4.1641.

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Abstract Although plasmids can provide beneficial functions to their host bacteria, they might confer a physiological or energetic cost. This study examines how natural selection may reduce the cost of carrying conjugative plasmids with drug-resistance markers in the absence of antibiotic selection. We studied two plasmids, R1 and RP4, both of which carry multiple drug resistance genes and were shown to impose an initial fitness cost on Escherichia coli. To determine if and how the cost could be reduced, we subjected plasmid-containing bacteria to 1100 generations of evolution in batch cultures. Analysis of the evolved populations revealed that plasmid loss never occurred, but that the cost was reduced through genetic changes in both the plasmids and the bacteria. Changes in the plasmids were inferred by the demonstration that evolved plasmids no longer imposed a cost on their hosts when transferred to a plasmid-free clone of the ancestral E. coli. Changes in the bacteria were shown by the lowered cost when the ancestral plasmids were introduced into evolved bacteria that had been cured of their (evolved) plasmids. Additionally, changes in the bacteria were inferred because conjugative transfer rates of evolved R1 plasmids were lower in the evolved host than in the ancestral host. Our results suggest that once a conjugative bacterial plasmid has invaded a bacterial population it will remain even if the original selection is discontinued.

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10

Mahan, M. J., and J. R. Roth. "Reciprocality of recombination events that rearrange the chromosome." Genetics 120, no. 1 (September 1, 1988): 23–35. http://dx.doi.org/10.1093/genetics/120.1.23.

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Abstract We describe a genetic system for studying the reciprocality of chromosomal recombination; all substrates and recombination functions involved are provided exclusively by the bacterial chromosome. The genetic system allows the recovery of both recombinant products from a single recombination event. The system was used to demonstrate the full reciprocality of three different types of recombination events: (1) intrachromosomal recombination between direct repeats, causing deletions; (2) intrachromosomal recombination between inverse homologies, causing inversion of a segment of the bacterial chromosome; and (3) circle to circle recombination (in the absence of any plasmid or phage functions). Results suggest that intrachromosomal recombination in bacteria is frequently fully reciprocal.

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11

Betley, M. J., V. L. Miller, and J. J. Mekalanos. "Genetics of Bacterial Enterotoxins." Annual Review of Microbiology 40, no. 1 (October 1986): 577–605. http://dx.doi.org/10.1146/annurev.mi.40.100186.003045.

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12

Tucker, Stephanie, and James Bliska. "Genetics of bacterial virulence." Trends in Microbiology 3, no. 1 (January 1995): 35–36. http://dx.doi.org/10.1016/s0966-842x(00)88867-8.

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13

Ingham, E. "Genetics of bacterial virulence." Biochemical Education 24, no. 2 (April 1996): 126–27. http://dx.doi.org/10.1016/0307-4412(96)88976-x.

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14

Beckwith, Jon. "Genetics of bacterial diversity." Trends in Genetics 5 (1989): 348. http://dx.doi.org/10.1016/0168-9525(89)90141-8.

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15

Danchin, A. "Genetics of bacterial diversity." Biochimie 74, no. 6 (June 1992): 594. http://dx.doi.org/10.1016/0300-9084(92)90173-c.

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16

Meighen, E. A. "Genetics of Bacterial Bioluminescence." Annual Review of Genetics 28, no. 1 (December 1994): 117–39. http://dx.doi.org/10.1146/annurev.ge.28.120194.001001.

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17

Mushegian, Arcady R., and Eugene V. Koonin. "Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains." Genetics 144, no. 2 (October 1, 1996): 817–28. http://dx.doi.org/10.1093/genetics/144.2.817.

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Abstract Most of the genes involved in the development of multicellular eukaryotes encode large, multidomain proteins. To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. This computational approach allowed us to detect previously unnoticed but potentially important sequence similarities. Developmental gene products are enriched in predicted nonglobular regions as compared to unbiased sets of eukaryotic and bacterial proteins. Developmental genes that act intracellularly, primarily at the level of transcription regulation, typically code for proteins containing highly conserved DNA-binding domains, most of which appear to have evolved before the radiation of bacteria and eukaryotes. We identified bacterial homologues, namely a protein family that includes the Escherichia coli universal stress protein UspA, for the MADS-box transcription regulators previously described only in eukaryotes. We also show that the FUS6 family of eukaryotic proteins contains a putative DNA-binding domain related to bacterial helix-turn-helix transcription regulators. Developmental proteins that act extracellularly are less conserved and often do not have bacterial homologues. Nevertheless, several provocative similarities between different groups of such proteins were detected.

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18

Perrot-Minnot, Marie-Jeanne, Li Rong Guo, and John H. Werren. "Single and Double Infections with Wolbachia in the Parasitic Wasp Nasonia vitripennis Effects on Compatibility." Genetics 143, no. 2 (June 1, 1996): 961–72. http://dx.doi.org/10.1093/genetics/143.2.961.

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Abstract Wolbachia are cytoplasmically inherited bacteria responsible for reproductive incompatibility in a wide range of insects. There has been little exploration, however, of within species Wolbachia polymorphisms and their effects on compatibility. Here we show that some strains of the parasitic wasp Nasonia vitripennis are infected with two distinct bacterial strains (A and B) whereas others are singly infected (A or B). Double and single infections are confirmed by both PCR amplification and Southern analysis of genomic DNA. Furthermore, it is shown that prolonged larval diapause (the overwintering stage of the wasp) of a double-infected strain can lead to stochastic loss of one or both bacterial strains. After diapause of a double-infected line, sublines were produced with AB, A only, B only or no Wolbachia. A and B sublines are bidirectionally incompatible, whereas males from AB lines are unidirectionally incompatible with females of A and B sublines. Results therefore show rapid development of bidirectional incompatibility within a species due to segregation of associated symbiotic bacteria.

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19

Kurmasheva, Naziia, Vyacheslav Vorobiev, Margarita Sharipova, Tatyana Efremova, and Ayslu Mardanova. "The Potential Virulence Factors ofProvidencia stuartii: Motility, Adherence, and Invasion." BioMed Research International 2018 (2018): 1–8. http://dx.doi.org/10.1155/2018/3589135.

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Providencia stuartiiis the most commonProvidenciaspecies capable of causing human infections. CurrentlyP. stuartiiis involved in high incidence of urinary tract infections in catheterized patients. The ability of bacteria to swarm on semisolid (viscous) surfaces and adhere to and invade host cells determines the specificity of the disease pathogenesis and its therapy. In the present study we demonstrated morphological changes ofP. stuartiiNK cells during migration on the viscous medium and discussed adhesive and invasive properties utilizing the HeLa-M cell line as a host model. To visualize the interaction ofP. stuartiiNK bacterial cells with eukaryotic cellsin vitroscanning electron and confocal microscopy were performed. We found that bacteriaP. stuartiiNK are able to adhere to and invade HeLa-M epithelial cells and these properties depend on the age of bacterial culture. Also, to invade the host cells the infectious dose of the bacteria is essential. The microphotographs indicate that after incubation of bacterialP. stuartiiNK cells together with epithelial cells the bacterial cells both were adhered onto and invaded into the host cells.

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20

Johnston, Mark. "Joshua Lederberg on Bacterial Recombination." Genetics 203, no. 2 (June 2016): 613–14. http://dx.doi.org/10.1534/genetics.116.190637.

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21

De Maio, Nicola, and Daniel J. Wilson. "The Bacterial Sequential Markov Coalescent." Genetics 206, no. 1 (March 3, 2017): 333–43. http://dx.doi.org/10.1534/genetics.116.198796.

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22

Turner, Paul E. "Phenotypic Plasticity in Bacterial Plasmids." Genetics 167, no. 1 (May 2004): 9–20. http://dx.doi.org/10.1534/genetics.167.1.9.

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23

Virolle, Chloé, Kelly Goldlust, Sarah Djermoun, Sarah Bigot, and Christian Lesterlin. "Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level." Genes 11, no. 11 (October 22, 2020): 1239. http://dx.doi.org/10.3390/genes11111239.

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Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.

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24

da Silva, Herculano, Tatiane M. P. Oliveira, and Maria Anice M. Sallum. "Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species." Genes 13, no. 11 (November 7, 2022): 2052. http://dx.doi.org/10.3390/genes13112052.

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Mosquitoes (Diptera: Culicidae) are found widely throughout the world. Several species can transmit pathogens to humans and other vertebrates. Mosquitoes harbor great amounts of bacteria, fungi, and viruses. The bacterial composition of the microbiota of these invertebrates is associated with several factors, such as larval habitat, environment, and species. Yet little is known about bacterial interaction networks in mosquitoes. This study investigates the bacterial communities of eight species of Culicidae collected in Vale do Ribeira (Southeastern São Paulo State) and verifies the bacterial interaction network in these species. Sequences of the 16S rRNA region from 111 mosquito samples were analyzed. Bacterial interaction networks were generated from Spearman correlation values. Proteobacteria was the predominant phylum in all species. Wolbachia was the predominant genus in Haemagogus leucocelaenus. Aedes scapularis, Aedes serratus, Psorophora ferox, and Haemagogus capricornii were the species that showed a greater number of bacterial interactions. Bacterial positive interactions were found in all mosquito species, whereas negative correlations were observed in Hg. leucocelaenus, Ae. scapularis, Ae. serratus, Ps. ferox, and Hg. capricornii. All bacterial interactions with Asaia and Wolbachia were negative in Aedes mosquitoes.

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25

Sprent, J. I., J. C. Fry, and M. J. Davy. "Bacterial Genetics in Natural Environments." Journal of Applied Ecology 29, no. 1 (1992): 261. http://dx.doi.org/10.2307/2404368.

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26

Berry, D. R. "Bacterial genetics in natural environments." Biochemical Systematics and Ecology 19, no. 1 (January 1991): 93. http://dx.doi.org/10.1016/0305-1978(91)90118-j.

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27

Kieft, Thomas L. "Bacterial genetics in natural environments." Trends in Genetics 7, no. 7 (July 1991): 236–37. http://dx.doi.org/10.1016/0168-9525(91)90373-x.

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28

Solioz, Marc, and Denise Bienz. "Bacterial genetics by electric shock." Trends in Biochemical Sciences 15, no. 5 (May 1990): 175–77. http://dx.doi.org/10.1016/0968-0004(90)90154-4.

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29

Symonds, N. "The emergence of bacterial genetics." Trends in Biochemical Sciences 16 (January 1991): 199–200. http://dx.doi.org/10.1016/0968-0004(91)90079-b.

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30

Krügel, H. "The Emergence of Bacterial Genetics." Journal of Electroanalytical Chemistry 342, no. 2 (April 1992): 239. http://dx.doi.org/10.1016/0022-0728(92)85055-8.

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31

Krügel, H. "The Emergence of Bacterial Genetics." Bioelectrochemistry and Bioenergetics 27, no. 2 (April 1992): 239. http://dx.doi.org/10.1016/0302-4598(92)87048-y.

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32

Silverman, Sanford J. "Experimental techniques in bacterial genetics." Analytical Biochemistry 192, no. 1 (January 1991): 254. http://dx.doi.org/10.1016/0003-2697(91)90219-j.

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33

Haubold, Bernhard, Michael Travisano, Paul B. Rainey, and Richard R. Hudson. "Detecting Linkage Disequilibrium in Bacterial Populations." Genetics 150, no. 4 (December 1, 1998): 1341–48. http://dx.doi.org/10.1093/genetics/150.4.1341.

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Abstract The distribution of the number of pairwise differences calculated from comparisons between n haploid genomes has frequently been used as a starting point for testing the hypothesis of linkage equilibrium. For this purpose the variance of the pairwise differences, VD, is used as a test statistic to evaluate the null hypothesis that all loci are in linkage equilibrium. The problem is to determine the critical value of the distribution of VD. This critical value can be estimated either by Monte Carlo simulation or by assuming that VD is distributed normally and calculating a one-tailed 95% critical value for VD, L, L = E(VD) + 1.645 Var(VD), where E(VD) is the expectation of VD, and Var(VD) is the variance of VD. If VD (observed) > L, the null hypothesis of linkage equilibrium is rejected. Using Monte Carlo simulation we show that the formula currently available for Var(VD) is incorrect, especially for genetically highly diverse data. This has implications for hypothesis testing in bacterial populations, which are often genetically highly diverse. For this reason we derive a new, exact formula for Var(VD). The distribution of VD is examined and shown to approach normality as the sample size increases. This makes the new formula a useful tool in the investigation of large data sets, where testing for linkage using Monte Carlo simulation can be very time consuming. Application of the new formula, in conjunction with Monte Carlo simulation, to populations of Bradyrhizobium japonicum, Rhizobium leguminosarum, and Bacillus subtilis reveals linkage disequilibrium where linkage equilibrium has previously been reported.

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34

Bertels, Frederic, Chaitanya S. Gokhale, and Arne Traulsen. "Discovering Complete Quasispecies in Bacterial Genomes." Genetics 206, no. 4 (June 19, 2017): 2149–57. http://dx.doi.org/10.1534/genetics.117.201160.

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35

Gregg, K., G. Allen, and C. Beard. "Genetic manipulation of rumen bacteria: from potential to reality." Australian Journal of Agricultural Research 47, no. 2 (1996): 247. http://dx.doi.org/10.1071/ar9960247.

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The development of techniques for manipulating the molecular genetics of bacteria led naturally to suggestions for using this technology to alter rumen function. Despite early difficulties, methods are now available to insert new genetic material into several rumen bacterial species, including Butyrivibrio fibrisolvens, Prevotella ruminicola, and Ruminococcus albus. One strain of B. fibrisolvens has been modified to detoxify a naturally occurring poison that causes major losses of livestock in Australia, Africa, and Central America. The stability of that modified organism has been demonstrated by its recolonization of the rumen and retention of its altered genotype over 5 months in vivo. Many of the persistent doubts about rumen bacterial genetic manipulation and the viability of altered organisms in a competitive environment have been shown to be capable of resolution, and interest in this area of research may be revitalized by these results. Apart from the achievement of specific metabolic improvements, the technology now available will allow extensive characterization of the molecular genetics of rumen bacteria with a precision that was not previously possible.

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36

Duncan, Margaret J. "Genomics of Oral Bacteria." Critical Reviews in Oral Biology & Medicine 14, no. 3 (May 2003): 175–87. http://dx.doi.org/10.1177/154411130301400303.

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Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators’ ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

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37

Accoti, Anastasia, Laura C. Multini, Babakar Diouf, Margaret Becker, Julia Vulcan, Massamba Sylla, Dianne Y. Yap, et al. "The influence of the larval microbiome on susceptibility to Zika virus is mosquito genotype-dependent." PLOS Pathogens 19, no. 10 (October 30, 2023): e1011727. http://dx.doi.org/10.1371/journal.ppat.1011727.

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The microbiome of the mosquito Aedes aegypti is largely determined by the environment and influences mosquito susceptibility for arthropod-borne viruses (arboviruses). Larval interactions with different bacteria can have carry-over effects on adult Ae. aegypti replication of arboviruses, but little is known about the role that mosquito host genetics play in determining how larval-bacterial interactions shape Ae aegypti susceptibility to arboviruses. To address this question, we isolated single bacterial isolates and complex microbiomes from Ae. aegypti larvae from various field sites in Senegal. Either single bacterial isolates or complex microbiomes were added to two different genetic backgrounds of Ae. aegypti in a gnotobiotic larval system. Using 16S amplicon sequencing we showed that the bacterial community structure differs between the two genotypes of Ae. aegypti when given identical microbiomes, and the abundance of single bacterial taxa differed between Ae. aegypti genotypes. Using single bacterial isolates or the entire preserved complex microbiome, we tested the ability of specific larval microbiomes to drive differences in infection rates for Zika virus in different genetic backgrounds of Ae. aegypti. We observed that the proportion of Zika virus-infected adults was dependent on the interaction between the larval microbiome and Ae. aegypti host genetics. By using the larval microbiome as a component of the environment, these results demonstrate that interactions between the Ae. aegypti genotype and its environment can influence Zika virus infection. As Ae. aegypti expands and adapts to new environments under climate change, an understanding of how different genotypes interact with the same environment will be crucial for implementing arbovirus transmission control strategies.

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38

Lederberg, J. "Replica plating and indirect selection of bacterial mutants: isolation of preadaptive mutants in bacteria by sib selection." Genetics 121, no. 3 (March 1, 1989): 395–99. http://dx.doi.org/10.1093/genetics/121.3.395.

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39

Giordano, R., S. L. O'Neill, and H. M. Robertson. "Wolbachia infections and the expression of cytoplasmic incompatibility in Drosophila sechellia and D. mauritiana." Genetics 140, no. 4 (August 1, 1995): 1307–17. http://dx.doi.org/10.1093/genetics/140.4.1307.

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Abstract Various stocks of Drosophila mauritiana and D. sechellia were found to be infected with Wolbachia, a Rickettsia-like bacterium that is known to cause cytoplasmic incompatibility and other reproductive abnormalities in arthropods. Testing for the expression of cytoplasmic incompatibility in these two species showed partial incompatibility in D. sechellia but no expression of incompatibility in D. mauritiana. To determine whether absence of cytoplasmic incompatibility in D. mauritiana was due to either the bacterial or host genome, we transferred bacteria from D. mauritiana into an uninfected strain of D. simulans, a host species known to express high levels of incompatibility with endogenous Wolbachia. We also performed the reciprocal transfer of the natural D. simulans Riverside infection into a tetracycline-treated stock of D. mauritiana. In each case, the ability to express incompatibility was unaltered by the different host genetic background. These experiments indicate that in D. simulans and D. mauritiana expression of the cytoplasmic incompatibility phenotype is determined by the bacterial strain and that D. mauritiana harbors a neutral strain of Wolbachia.

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40

Anderson, Eric C., and Paul A. Scheet. "Improving the Estimation of Bacterial Allele Frequencies." Genetics 158, no. 3 (July 1, 2001): 1383–86. http://dx.doi.org/10.1093/genetics/158.3.1383.

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41

Feinstein, Sheldon I., and K. Brooks Low. "HYPER-RECOMBINING RECIPIENT STRAINS IN BACTERIAL CONJUGATION." Genetics 113, no. 1 (May 1, 1986): 13–33. http://dx.doi.org/10.1093/genetics/113.1.13.

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ABSTRACT Using a direct enrichment and screening procedure, mutants of Escherichia coli have been isolated in which recombination frequencies for several intragenic Hfr × F- crosses are significantly higher (twofold to sixfold) than in the parental strains. These hyper-recombination mutations comprised five new mutS - and one new mutL - allele. Together with other known mut - alleles, they were analyzed for effects on intragenic recombination using several types of crosses. Hyper-recombination was found for mutS -, mutL -, mutH (=mutR)- and mutU (=uvrD)-, with the largest effects seen for certain alleles of uvrD; these resulted in over 20-fold excesses in recombinant production for Hfr × F- crosses and F'-chromosome homogenotization. Spontaneous mutator ability was not always correlated with degree of hyper-recombination.

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42

Arber. "Self-Organization of the Biological Evolution." Genes 10, no. 11 (October 28, 2019): 854. http://dx.doi.org/10.3390/genes10110854.

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We report here experiments carried out with nonpathogenic Escherichia coli bacterial strains and their phages. This research yielded interesting insights into their activities, occasionally producing genetic variants of different types. In order to not interfere with the genetic stability of the parental strains involved, we found that the bacteria are genetically equipped to only rarely produce a genetic variant, which may occur by a number of different approaches. On the one hand, the genes of relevance for the production of specific genetic variants are relatively rarely expressed. On the other hand, other gene products act as moderators of the frequencies that produce genetic variants. We call the genes producing genetic variants and those moderating the frequencies of genetic variation “evolution genes”. Their products are generally not required for daily bacterial life. We can, therefore, conclude that the bacterial genome has a duality. Some of the bacterial enzymes involved in biological evolution have become useful tools (e.g., restriction endonucleases) for molecular genetic research involving the genetic set-up of any living organism.

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43

Achaz, Guillaume, Eric Coissac, Pierre Netter, and Eduardo P. C. Rocha. "Associations Between Inverted Repeats and the Structural Evolution of Bacterial Genomes." Genetics 164, no. 4 (August 1, 2003): 1279–89. http://dx.doi.org/10.1093/genetics/164.4.1279.

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Abstract The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong underrepresentation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

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44

Ilicic, Doris, Danny Ionescu, Jason Woodhouse, and Hans-Peter Grossart. "Temperature-Related Short-Term Succession Events of Bacterial Phylotypes in Potter Cove, Antarctica." Genes 14, no. 5 (May 8, 2023): 1051. http://dx.doi.org/10.3390/genes14051051.

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In recent years, our understanding of the roles of bacterial communities in the Antarctic Ocean has substantially improved. It became evident that Antarctic marine bacteria are metabolically versatile, and even closely related strains may differ in their functionality and, therefore, affect the ecosystem differently. Nevertheless, most studies have been focused on entire bacterial communities, with little attention given to individual taxonomic groups. Antarctic waters are strongly influenced by climate change; thus, it is crucial to understand how changes in environmental conditions, such as changes in water temperature and salinity fluctuations, affect bacterial species in this important area. In this study, we show that an increase in water temperature of 1 °C was enough to alter bacterial communities on a short-term temporal scale. We further show the high intraspecific diversity of Antarctic bacteria and, subsequently, rapid intra-species succession events most likely driven by various temperature-adapted phylotypes. Our results reveal pronounced changes in microbial communities in the Antarctic Ocean driven by a single strong temperature anomaly. This suggests that long-term warming may have profound effects on bacterial community composition and presumably functionality in light of continuous and future climate change.

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45

Muhammadi and Nuzhat Ahmed. "Genetics of Bacterial Alginate: Alginate Genes Distribution, Organization and Biosynthesis in Bacteria." Current Genomics 8, no. 3 (May 1, 2007): 191–202. http://dx.doi.org/10.2174/138920207780833810.

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46

Vasse, Marie, and Sébastien Wielgoss. "Bacteriophages of Myxococcus xanthus, a Social Bacterium." Viruses 10, no. 7 (July 18, 2018): 374. http://dx.doi.org/10.3390/v10070374.

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Bacteriophages have been used as molecular tools in fundamental biology investigations for decades. Beyond this, however, they play a crucial role in the eco-evolutionary dynamics of bacterial communities through their demographic impact and the source of genetic information they represent. The increasing interest in describing ecological and evolutionary aspects of bacteria–phage interactions has led to major insights into their fundamental characteristics, including arms race dynamics and acquired bacterial immunity. Here, we review knowledge on the phages of the myxobacteria with a major focus on phages infecting Myxococcus xanthus, a bacterial model system widely used to study developmental biology and social evolution. In particular, we focus upon the isolation of myxophages from natural sources and describe the morphology and life cycle parameters, as well as the molecular genetics and genomics of the major groups of myxophages. Finally, we propose several interesting research directions which focus on the interplay between myxobacterial host sociality and bacteria–phage interactions.

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47

Draghi, Jeremy A., and Paul E. Turner. "DNA secretion and gene-level selection in bacteria." Microbiology 152, no. 9 (September 1, 2006): 2683–88. http://dx.doi.org/10.1099/mic.0.29013-0.

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Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.

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48

Redfield, Rosemary J., Matthew R. Schrag, and Antony M. Dean. "The Evolution of Bacterial Transformation: Sex With Poor Relations." Genetics 146, no. 1 (May 1, 1997): 27–38. http://dx.doi.org/10.1093/genetics/146.1.27.

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Bacteria are the only organisms known to actively take up DNA and recombine it into their genomes. While such natural transformation systems may provide many of the same benefits that sexual reproduction provides eukaryotes, there are important differences that critically alter the consequences, especially when recombination's main benefit is reducing the mutation load. Here, analytical and numerical methods are used to study the selection of transformation genes in populations undergoing deleterious mutation. Selection for transformability depends on the shape of the fitness function against mutation. If the fitness function is linear, then transformation would be selectively neutral were it not for the possibility that transforming cells may take up DNA that converts them into nontransformable cells. If the selection includes strong positive (synergistic) epistasis, then transformation can be advantageous in spite of this risk. The effect of low quality DNA (from selectively killed cells) on selection is then studied analytically and found to impose an additional cost. The limited data available for real bacterial populations suggest that the conditions necessary for the evolution of transformation are unlikely to be met, and thus that DNA uptake may have some function other than recombination of deleterious mutations.

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49

Maloy, Stanley, and Thomas Zahrt. "Surrogate Genetics: The Use of Bacterial Hybrids as a Genetic Tool." Methods 20, no. 1 (January 2000): 73–79. http://dx.doi.org/10.1006/meth.1999.0907.

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50

Spratt, Brian G., and Martin C. J. Maiden. "Bacterial population genetics, evolution and epidemiology." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1384 (April 29, 1999): 701–10. http://dx.doi.org/10.1098/rstb.1999.0423.

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Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non–clonal, most containing both clonal and non–clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies.

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