Microbial genetics

Microbial genetics is a subject area within microbiology and genetic engineering. It studies the genetics of very small (micro) organisms; bacteria, archaea, viruses and some protozoa and fungi.[1] This involves the study of the genotype of microbial species and also the expression system in the form of phenotypes.

Since the discovery of microorganisms by two Fellows of The Royal Society, Robert Hooke and Antoni van Leeuwenhoek during the period 1665-1885[2] they have been used to study many processes and have had applications in various areas of study in genetics. For example: Microorganisms' rapid growth rates and short generation times are used by scientists to study evolution.[3] Microbial genetics also has applications in being able to study processes and pathways that are similar to those found in humans such as drug metabolism.[4]

Microorganisms whose study is encompassed by microbial genetics

Bacteria

Bacteria are classified by their shape.

Bacteria have been on this planet for approximately 3.5 billion years, and are classified by their shape.[5] Bacterial genetics studies the mechanisms of their heritable information, their chromosomes, plasmids, transposons, and phages.[6]

Gene transfer systems that have been extensively studied in bacteria include genetic transformation, conjugation and transduction. Natural transformation is a bacterial adaptation for DNA transfer between two cells through the intervening medium. The uptake of donor DNA and its recombinational incorporation into the recipient chromosome depends on the expression of numerous bacterial genes whose products direct this process.[7][8] In general, transformation is a complex, energy-requiring developmental process that appears to be an adaptation for repairing DNA damage.[9]

Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. Bacterial conjugation has been extensively studied in Escherichia coli, but also occurs in other bacteria such as Mycobacterium smegmatis. Conjugation requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. E. coli conjugation is mediated by expression of plasmid genes, whereas mycobacterial conjugation is mediated by genes on the bacterial chromosome.[10]

Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector. Transduction is a common tool used by molecular biologists to stably introduce a foreign gene into a host cell's genome.

Archaea

Archaea is a domain of organisms that are prokaryotic, single-celled, and are thought to have developed 4 billion years ago. They share a common ancestor with bacteria, but are more closely related to eukaryotes in comparison to bacteria.[11] Some Archaea are able to survive extreme environments, which leads to many applications in the field of genetics. One of such applications is the use of archaeal enzymes, which would be better able to survive harsh conditions in vitro.[12]

Gene transfer and genetic exchange have been studied in the halophilic archaeon Halobacterium volcanii and the hyperthermophilic archaeons Sulfolobus solfataricus and Sulfolobus acidocaldarius. H. volcani forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.[13] When S. solfataricus and S. acidocaldarius are exposed to DNA damaging agents, species-specific cellular aggregation is induced. Cellular aggregation mediates chromosomal marker exchange and genetic recombination with high frequency. Cellular aggregation is thought to enhance species specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination.[14][15][16]

Fungi

Fungi can be both multicellular and unicellular organisms, and are distinguished from other microbes by the way they obtain nutrients. Fungi secrete enzymes into their surroundings, to break down organic matter.[5] Fungal genetics uses yeast, and filamentous fungi as model organisms for eukaryotic genetic research, including cell cycle regulation, chromatin structure and gene regulation.[17]

Studies of the fungus Neurospora crassa have contributed substantially to understanding how genes work. N. crassa is a type of red bread mold of the phylum Ascomycota. It is used as a model organism because it is easy to grow and has a haploid life cycle that makes genetic analysis simple since recessive traits will show up in the offspring. Analysis of genetic recombination is facilitated by the ordered arrangement of the products of meiosis in ascospores. In its natural environment, N. crassa lives mainly in tropical and sub-tropical regions. It often can be found growing on dead plant matter after fires.

Neurospora was used by Edward Tatum and George Beadle in their experiments[18] for which they won the Nobel Prize in Physiology or Medicine in 1958. The results of these experiments led directly to the one gene-one enzyme hypothesis that specific genes code for specific proteins. This concept proved to be the opening gun in what became molecular genetics and all the developments that have followed from that.[19]

Saccharomyces cerevisiae is a yeast of the phylum Ascomycota. During vegetative growth that ordinarily occurs when nutrients are abundant, S. cerevisiae reproduces by mitosis as diploid cells. However, when starved, these cells undergo meiosis to form haploid spores.[20] Mating occurs when haploid cells of opposite mating types MATa and MATα come into contact. Ruderfer et al.[21] pointed out that, in nature, such contacts are frequent between closely related yeast cells for two reasons. The first is that cells of opposite mating type are present together in the same acus, the sac that contains the cells directly produced by a single meiosis, and these cells can mate with each other. The second reason is that haploid cells of one mating type, upon cell division, often produce cells of the opposite mating type. An analysis of the ancestry of natural S. cerevisiae strains concluded that outcrossing occurs very infrequently (only about once every 50,000 cell divisions).[21] The relative rarity in nature of meiotic events that result from outcrossing suggests that the possible long-term benefits of outcrossing (e.g. generation of diversity) are unlikely to be sufficient for generally maintaining sex from one generation to the next. Rather, a short term benefit, such as meiotic recombinational repair of DNA damages caused by stressful conditions (such as starvation)[22][23][24] may be the key to the maintenance of sex in S. cerevisiae.

Candida albicans is a diploid fungus that grows both as a yeast and as a filament. C. albicans is the most common fungal pathogen in humans. It causes both debilitating mucosal infections and potentially life-threatening systemic infections. C. albicans has maintained an elaborate, but largely hidden, mating apparatus.[25] Johnson[25] suggested that mating strategies may allow C. albicans to survive in the hostile environment of a mammalian host.

Among the 250 known species of aspergilli, about 33% have an identified sexual state.[26] Among those Aspergillus species that exhibit a sexual cycle the overwhelming majority in nature are homothallic (self-fertilizing).[26] Selfing in the homothallic fungus Aspergillus nidulans involves activation of the same mating pathways characteristic of sex in outcrossing species, i.e. self-fertilization does not bypass required pathways for outcrossing sex but instead requires activation of these pathways within a single individual.[27] Fusion of haploid nuclei occurs within reproductive structures termed cleistothecia, in which the diploid zygote undergoes meiotic divisions to yield haploid ascospores.

Protozoa

Protozoa are unicellular organisms, which have nuclei, and ultramicroscopic cellular bodies within their cytoplasm.[5] One particular aspect of protozoa that are of interest to human geneticists are their flagella, which are very similar to human sperm flagella.

Studies of Paramecia have contributed to our understanding of the function of meiosis. Like all ciliates, Paramecia have a polyploid macronucleus, and one or more diploid micronuclei. The macronucleus controls non-reproductive cell functions, expressing the genes needed for daily functioning. The micronucleus is the generative, or germline nucleus, containing the genetic material that is passed along from one generation to the next.[28]

In the asexual fission phase of growth, during which cell divisions occur by mitosis rather than meiosis, clonal aging occurs leading to a gradual loss of vitality. In some species, such as the well studied Paramecium tetraurelia, the asexual line of clonally aging paramecia loses vitality and expires after about 200 fissions if the cells fail to undergo meiosis followed by either autogamy (self-fertilizaion) or conjugation (outcrossing) (see aging in Paramecium). DNA damage increases dramatically during successive clonal cell divisions and is a likely cause of clonal aging in P. tetraurelia.[29][30][31]

When clonally aged P. tetraurelia are stimulated to undergo meiosis in association with either autogamy or conjugation, the progeny are rejuvenated, and are able to have many more mitotic binary fission divisions. During either of these processes the micronuclei of the cell(s) undergo meiosis, the old macronucleus disintegrates and a new macronucleus is formed by replication of the micronuclear DNA that had recently undergone meiosis. There is apparently little, if any, DNA damage in the new macronucleus, suggesting that rejuvenation is associated with the repair of these damages in the micronucleus during meiosis.[24]

Viruses

Viruses are capsid-encoding organisms composed of proteins and nucleic acids that can self-assemble after replication in a host cell using the host's replication machinery.[32] There is a disagreement in science about whether viruses are living due to their lack of ribosomes.[32] Comprehending the viral genome is important not only for studies in genetics but also for understanding their pathogenic properties.[33]

Many types of virus are capable of genetic recombination. When two or more individual viruses of the same type infect a cell, their genomes may recombine with each other to produce recombinant virus progeny. Both DNA and RNA viruses can undergo recombination. When two or more viruses, each containing lethal genomic damage infect the same host cell, the virus genomes often can pair with each other and undergo homologous recombinational repair to produce viable progeny.[34][35] This process is known as multiplicity reactivation.[34][36] Enzymes employed in multiplicity reactivation are functionally homologous to enzymes employed in bacterial and eukaryotic recombinational repair. Multiplicity reactivation has been found to occur with pathogenic viruses including influenza virus, HIV-1, adenovirus simian virus 40, vaccinia virus, reovirus, poliovirus and herpes simplex virus as well as numerous bacteriophages.[36]

Applications of microbial genetics

Taq polymerase which is used in Polymerase Chain Reaction(PCR)

Microbes are ideally suited for biochemical and genetics studies and have made huge contributions to these fields of science such as the demonstration that DNA is the genetic material,[37][38] that the gene has a simple linear structure,[39] that the genetic code is a triplet code,[40] and that gene expression is regulated by specific genetic processes.[41] Jacques Monod and François Jacob used Escherichia coli, a type of bacteria, in order to develop the operon model of gene expression, which lay down the basis of gene expression and regulation.[42] Furthermore the hereditary processes of single-celled eukaryotic microorganisms are similar to those in multi-cellular organisms allowing researchers to gather information on this process as well.[43] Another bacterium which has greatly contributed to the field of genetics is Thermus aquaticus, which is a bacterium that tolerates high temperatures. From this microbe scientists isolated the enzyme Taq polymerase, which is now used in the powerful experimental technique, Polymerase chain reaction(PCR).[44] Additionally the development of recombinant DNA technology through the use of bacteria has led to the birth of modern genetic engineering and biotechnology.[5]

Using microbes, protocols were developed to insert genes into bacterial plasmids, taking advantage of their fast reproduction, to make biofactories for the gene of interest. Such genetically engineered bacteria can produce pharmaceuticals such as insulin, human growth hormone, interferons and blood clotting factors.[5] Microbes synthesize a variety of enzymes for industrial applications, such as fermented foods, laboratory test reagents, dairy products (such as renin), and even in clothing (such as Trichoderma fungus whose enzyme is used to give jeans a stone washed appearance).[5]

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