LTTRs: Big Players in Bacterial Gene Regulation
Dr. Stephanie M. Prezioso
Many qualities of all living organisms are determined by their genetic information. To accomplish this, many genes are translated into proteins that can carry out specific functions within a cell. However, only some genes within a cell are being translated into protein at any given time, and complex mechanisms exist to turn genes on or off as the cell needs. This control is called regulation of gene expression, and it drives processes such as cellular differentiation and responses to changes in the environment. For example, each cell in your body carries the same genome, however, the cells in your skin have a different pattern of active genes than the cells that make up your liver, which allows these two genetically identical organs to carry out different functions in your body . In bacteria, encountering a food source in the environment will turn on the genes that code for the enzymes needed to break down the food source into useable energy [2, 3]. This regulation allows a bacterium to ration its resources, by only translating some genes into proteins depending on the available food source.
These genetic regulatory processes differ between the two classifications of life: Eukarya (animals, plants, fungi, and protists), and Prokarya (bacteria and archaea). In Prokaryotic organisms, there is a large set of proteins that regulate gene expression. These are the LysR Type Transcriptional Regulators (LTTR), which encompasses a group of more than 100 different genetic regulators. All of these LTTRs evolved from a common ancestor and have diversified over time to regulate different sets of genes . LTTRs are paramount for gene regulation in bacteria, as they are responsible for regulating genes involved in a wide variety of cellular processes including cellular metabolism , virulence , cell division , cell mobility , and sensing population density  among others.
Most LTTRs are activators of gene expression, and work by directly binding to the DNA near a gene or gene cluster to turn the genes “on” so they will make functional proteins. However, the precise way that they activate genes can be complicated and quite diverse. An example of this complexity are “inducers”, which are a small molecules that many LTTRs can bind, to turn on genes . This ultimately allows for a genetic response to the small molecule inducer. The inducer often has some relation to the genes being activated, resulting in LTTR driven feedback loops . An example of a positive feedback loop is the melting of the polar ice caps: as the ice melts, there is less reflection of solar light and the exposed water will absorb more heat from the sun, resulting in further melting of the ice caps, and so on. A similar positive feedback loop is observed in the bacteria Pseudomonas putida, a species capable of degrading the environmental pollutant naphthalene. The degradation of naphthalene by Pseudomonas putida produces an inducer molecule that binds to an LTTR called NahR. Once bound to its inducer, NahR turns on the genes for further naphthalene degradation . When the source of naphthalene is depleted, inducer levels will decrease, and NahR will not activate the naphthalene degradation genes. In this instance, Pseudomonas putida conserves resources by only activating the genes involved in naphthalene degradation when naphthalene is present.
Some LTTRs have been shown to regulate antibiotic resistance genes or virulence genes in pathogenic bacterial species including Escherichia coli [12, 13], Vibrio cholerae [6, 14], Pseudomonas aeruginosa [9, 15], Salmonella typhimurium [16, 17], and Yersinia pseudotuberculosis . In Pseudomonas aeruginosa, the multi-drug resistant human pathogen, LTTRs regulate both antibiotic resistance and virulence. When P. aeruginosa encounters β-lactam type antibiotics, an LTTR (named AmpR) turns on the gene to make the protein that is needed to break down the antibiotic, rendering the antibiotic ineffective . Additionally, when P. aeruginosa contacts the human cells it’s infecting a second LTTR (named BvlR) turns on a slew of genes that are involved in the production of toxins, needle-like systems that help infect human cells, and a protective colony formation called biofilm . If these two LTTRs are non-functional, P. aeruginosa becomes susceptible to β-lactam type antibiotics  and unable to efficiently cause disease . Although strong associations have been made between multiple LTTRs and the ability for bacteria to cause disease, the small molecule inducers that directly affect the activity of these LTTRs have not been identified in most cases [12, 14-16, 18].
LTTRs play significant roles in regulating a variety of important bacterial processes, and the study of these genetic regulators brings to light some interesting applications. Many bacterial genes still have unknown functions, yet studying the LTTRs that regulate them may help determine their functions. Considering the LTTR is likely to bind to an inducer molecule related to the functions of the genes that it regulates, LTTRs can be screened for inducers that may provide clues towards the functions of the regulated genes. Additionally, as bacteria are growing resistant to our current plethora of antibiotics , new strategies are being investigated that inhibit bacterial virulence without compromising bacterial growth to prevent drug resistance . Inhibition of virulence is thought to result in less selective pressure for the bacteria to develop resistance, since the organism’s survival is not at stake. LTTRs represent attractive targets for these virulence inhibition strategies, since a single LTTR can affect many virulence genes [22, 23]. Towards this end, concurrent research identifying the small molecule inducers for the LTTRs involved in virulence will assist with developing inhibitors of LTTR function. As the functions of many LTTRs remain to be determined, research on this diverse family of genetic regulators will continue to increase our understanding of gene regulation in bacteria.
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