Natural competence

Last updated
Natural competence. 1-Bacterial cell DNA 2-Bacterial cell plasmids 3-Sex pili 4-Plasmid of foreign DNA from a dead cell 5-Bacterial cell restriction enzyme 6-Unwound foreign plasmid 7-DNA ligase I: A plasmid of foreign DNA from a dead cell is intercepted by the sex pili of a naturally competent bacterial cell. II: The foreign plasmid is transduced through the sex pili into the bacterial cell, where it is processed by bacterial cell restriction enzymes. The restriction enzymes break the foreign plasmid into a strand of nucleotides that can be added to the bacterial DNA. III: DNA ligase integrates the foreign nucleotides into the bacterial cell DNA. IV: Recombination is complete and the foreign DNA has integrated into the original bacterial cell's DNA and will continue to be a part of it when the bacterial cell replicates next. Natural Competence Drawing.svg
Natural competence.
1-Bacterial cell DNA
2-Bacterial cell plasmids
3-Sex pili
4-Plasmid of foreign DNA from a dead cell
5-Bacterial cell restriction enzyme
6-Unwound foreign plasmid
7-DNA ligase
I: A plasmid of foreign DNA from a dead cell is intercepted by the sex pili of a naturally competent bacterial cell.
II: The foreign plasmid is transduced through the sex pili into the bacterial cell, where it is processed by bacterial cell restriction enzymes. The restriction enzymes break the foreign plasmid into a strand of nucleotides that can be added to the bacterial DNA.
III: DNA ligase integrates the foreign nucleotides into the bacterial cell DNA.
IV: Recombination is complete and the foreign DNA has integrated into the original bacterial cell's DNA and will continue to be a part of it when the bacterial cell replicates next.

In microbiology, genetics, cell biology, and molecular biology, competence is the ability of a cell to alter its genetics by taking up extracellular DNA from its environment through a process called transformation. Competence can be differentiated between natural competence and induced or artificial competence. Natural competence is a genetically specified ability of bacteria that occurs under natural conditions as well as in the laboratory. Artificial competence arises when cells in laboratory cultures are treated to make them transiently permeable to DNA. Competence allows for rapid adaptation and DNA repair of the cell.

Contents

History

Natural competence was discovered by Frederick Griffith in 1928, when he showed that a preparation of killed cells of a pathogenic bacterium contained something that could transform related non-pathogenic cells into the pathogenic type. [1] [2] In 1944 Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that this 'transforming factor' was pure DNA. [2] [3] This was the first compelling evidence that DNA carries the genetic information of the cell.

Since then, natural competence has been studied in a number of different bacteria, particularly Bacillus subtilis , Streptococcus pneumoniae , Neisseria gonorrhoeae , Haemophilus influenzae and members of the Acinetobacter genus. [1] Areas of active research include the mechanisms of DNA transport, the regulation of competence in different bacteria, and the evolutionary function of competence.

Mechanisms of DNA uptake

In the laboratory, DNA is provided by the researcher, often as a genetically engineered fragment or plasmid. During uptake, DNA is transported across the cell membrane(s), and the cell wall if one is present. Once the DNA is inside the cell it may be degraded to nucleotides, which are reused for DNA replication and other metabolic functions. Alternatively it may be recombined into the cell's genome by its DNA repair enzymes. If this recombination changes the cell's genotype the cell is said to have been transformed. Artificial competence and transformation are used as research tools in many organisms. [4]

In almost all naturally competent bacteria components of extracellular filaments called type IV pili bind extracellular double stranded DNA. The DNA is then translocated across the membrane (or membranes for gram negative bacteria) through multi-component protein complexes driven by the degradation of one strand of the DNA. Single stranded DNA in the cell is bound by a well-conserved protein, DprA, which loads the DNA onto RecA, which mediates homologous recombination through the classic DNA repair pathway. [5]

Regulation of competence

In laboratory cultures, natural competence is usually tightly regulated and often triggered by nutritional shortages or adverse conditions. However, the specific inducing signals and regulatory machinery are much more variable than the uptake machinery, regulation systems can vary in different species. [6] [1] Transcription factors have been discovered which regulate competence; an example is sxy (also known as tfoX) which has been found to be regulated in turn by a 5' non-coding RNA element. [7] In bacteria capable of forming spores, conditions inducing sporulation often overlap with those inducing competence. [1] [8] Thus cultures or colonies containing sporulating cells often also contain competent cells.

Most naturally competent bacteria are thought to take up all DNA molecules with roughly equal efficiencies. [1] However, bacteria in some families, such as Neisseriaceae and Pasteurellaceae, preferentially take up DNA fragments containing uptake signal sequences, which are short sequences that are frequent in their own genomes. [1] In Neisseriaceae these sequences are referred as DNA uptake sequence (DUS), while in Pasteurellaceae they're termed uptake signal sequence (USS). Neisserial genomes contain thousands of copies of the preferred sequence GCCGTCTGAA, and Pasteurellacean genomes contain either AAGTGCGGT or ACAAGCGGT. [4] [9]

Evolutionary functions and consequences of competence

Most proposals made for the primary evolutionary function of natural competence as a part of natural bacterial transformation fall into three categories: (1) the selective advantage of genetic diversity; (2) DNA uptake as a source of nucleotides (DNA as “food”); and (3) the selective advantage of a new strand of DNA to promote homologous recombinational repair of damaged DNA (DNA repair). It is possible that multiple proposals are true for different organisms. [1] A secondary suggestion has also been made, noting the occasional advantage of horizontal gene transfer.

Hypothesis of genetic diversity

According to one hypothesis, bacterial transformation may play the same role in increasing genetic diversity that sex plays in higher organisms. [1] [10] [11] However, the theoretical difficulties associated with the evolution of sex suggest that sex for genetic diversity is problematic. In the case of bacterial transformation, competence requires the high cost of a global protein synthesis switch, with, for example, more than 16 genes that are switched on only during competence of Streptococcus pneumoniae. [12] However, since bacteria tend to grow in clones, the DNA available for transformation would generally have the same genotype as that of the recipient cells. [13] Thus, there is always a high cost in protein expression without, in general, an increase in diversity. Other differences between competence and sex have been considered in models of the evolution of genes causing competence. These models found that competence's postulated recombinational benefits were even more elusive than those of sex. [13]

Hypothesis of DNA as food

The second hypothesis, DNA as food, relies on the fact that cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesize, these may make a significant contribution to the cell's energy budget. [14] Some naturally competent bacteria also secrete nucleases into their surroundings, and all bacteria can take up the free nucleotides these nucleases generate from environmental DNA. [15] The energetics of DNA uptake are not understood in any system, so it is difficult to compare the efficiency of nuclease secretion to that of DNA uptake and internal degradation. In principle the cost of nuclease production and the uncertainty of nucleotide recovery must be balanced against the energy needed to synthesize the uptake machinery and to pull DNA in. Other important factors are the likelihoods that nucleases and competent cells will encounter DNA molecules, the relative inefficiencies of nucleotide uptake from the environment and from the periplasm (where one strand is degraded by competent cells), and the advantage of producing ready-to-use nucleotide monophosphates from the other strand in the cytoplasm. Another complicating factor is the self-bias of the DNA uptake systems of species in the family Pasteurellaceae and the genus Neisseria, which could reflect either selection for recombination or for mechanistically efficient uptake. [16] [17]

Hypothesis of repair of DNA damage

In bacteria, the problem of DNA damage is most pronounced during periods of stress, particularly oxidative stress, that occur during crowding or starvation conditions. Some bacteria induce competence under such stress conditions, supporting the hypothesis that transformation helps DNA repair. [1] In experimental tests, bacterial cells exposed to agents damaging their DNA, and then undergoing transformation, survived better than cells exposed to DNA damage that did not undergo transformation. [18] In addition, competence to undergo transformation is often inducible by known DNA damaging agents. [19] [20] [1] Thus, a strong short-term selective advantage for natural competence and transformation would be its ability to promote homologous recombinational DNA repair under conditions of stress.

Horizontal gene transfer

A long-term advantage may occasionally be conferred by occasional instances of horizontal gene transfer also called lateral gene transfer, (which might result from non-homologous recombination after competence is induced), that could provide for antibiotic resistance or other advantages.

Regardless of the nature of selection for competence, the composite nature of bacterial genomes provides abundant evidence that the horizontal gene transfer caused by competence contributes to the genetic diversity that makes evolution possible.

See also

Related Research Articles

<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Horizontal gene transfer</span> Transfer of genes from unrelated organisms

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher-order evolution while more significantly shifting perspectives on bacterial evolution.

<i>Neisseria</i> Genus of bacteria

Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, N. meningitidis and N. gonorrhoeae.

The restriction modification system is found in bacteria and archaea, and provides a defense against foreign DNA, such as that borne by bacteriophages.

<span class="mw-page-title-main">Molecular genetics</span> Scientific study of genes at the molecular level

Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens. 

<span class="mw-page-title-main">Genetic transformation</span> Genetic alteration of a cell by uptake of genetic material from the environment

In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacterium must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory.

A mating system is a way in which a group is structured in relation to sexual behaviour. The precise meaning depends upon the context. With respect to animals, the term describes which males and females mate under which circumstances. Recognised systems include monogamy, polygamy, and promiscuity, all of which lead to different mate choice outcomes and thus these systems affect how sexual selection works in the species which practice them. In plants, the term refers to the degree and circumstances of outcrossing. In human sociobiology, the terms have been extended to encompass the formation of relationships such as marriage.

<i>Mycobacterium smegmatis</i> Species of bacterium

Mycobacterium smegmatis is an acid-fast bacterial species in the phylum Actinomycetota and the genus Mycobacterium. It is 3.0 to 5.0 μm long with a bacillus shape and can be stained by Ziehl–Neelsen method and the auramine-rhodamine fluorescent method. It was first reported in November 1884 by Lustgarten, who found a bacillus with the staining appearance of tubercle bacilli in syphilitic chancres. Subsequent to this, Alvarez and Tavel found organisms similar to that described by Lustgarten also in normal genital secretions (smegma). This organism was later named M. smegmatis.

<span class="mw-page-title-main">RecA</span> DNA repair protein

RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA in bacteria. Structural and functional homologs to RecA have been found in all kingdoms of life. RecA serves as an archetype for this class of homologous DNA repair proteins. The homologous protein is called RAD51 in eukaryotes and RadA in archaea.

<span class="mw-page-title-main">Homologous recombination</span> Genetic recombination between identical or highly similar strands of genetic material

Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.

Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.

Uptake signal sequences (USS) are short DNA sequences preferentially taken up by competent bacteria of the family Pasteurellaceae. Similar sequences, called DNA uptake sequences (DUS), are found in species of the family Neisseriaceae.

<span class="mw-page-title-main">Gene targeting</span> Genetic technique that uses homologous recombination to change an endogenous gene

Gene targeting is a biotechnological tool used to change the DNA sequence of an organism. It is based on the natural DNA-repair mechanism of Homology Directed Repair (HDR), including Homologous Recombination. Gene targeting can be used to make a range of sizes of DNA edits, from larger DNA edits such as inserting entire new genes into an organism, through to much smaller changes to the existing DNA such as a single base-pair change. Gene targeting relies on the presence of a repair template to introduce the user-defined edits to the DNA. The user will design the repair template to contain the desired edit, flanked by DNA sequence corresponding (homologous) to the region of DNA that the user wants to edit; hence the edit is targeted to a particular genomic region. In this way Gene Targeting is distinct from natural homology-directed repair, during which the ‘natural’ DNA repair template of the sister chromatid is used to repair broken DNA. The alteration of DNA sequence in an organism can be useful in both a research context – for example to understand the biological role of a gene – and in biotechnology, for example to alter the traits of an organism.

Calcium chloride (CaCl2) transformation is a laboratory technique in prokaryotic (bacterial) cell biology. The addition of calcium chloride to a cell suspension promotes the binding of plasmid DNA to lipopolysaccharides (LPS). Positively charged calcium ions attract both the negatively charged DNA backbone and the negatively charged groups in the LPS inner core. The plasmid DNA can then pass into the cell upon heat shock, where chilled cells (+4 degrees Celsius) are heated to a higher temperature (+42 degrees Celsius) for a short time.

The origin and function of meiosis are currently not well understood scientifically, and would provide fundamental insight into the evolution of sexual reproduction in eukaryotes. There is no current consensus among biologists on the questions of how sex in eukaryotes arose in evolution, what basic function sexual reproduction serves, and why it is maintained, given the basic two-fold cost of sex. It is clear that it evolved over 1.2 billion years ago, and that almost all species which are descendants of the original sexually reproducing species are still sexual reproducers, including plants, fungi, and animals.

<span class="mw-page-title-main">Genome editing</span> Type of genetic engineering

Genome editing, or genome engineering, or gene editing, is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism. Unlike early genetic engineering techniques that randomly inserts genetic material into a host genome, genome editing targets the insertions to site-specific locations. The basic mechanism involved in genetic manipulations through programmable nucleases is the recognition of target genomic loci and binding of effector DNA-binding domain (DBD), double-strand breaks (DSBs) in target DNA by the restriction endonucleases, and the repair of DSBs through homology-directed recombination (HDR) or non-homologous end joining (NHEJ).

<span class="mw-page-title-main">Genetic engineering techniques</span> Methods used to change the DNA of organisms

Genetic engineering techniques allow the modification of animal and plant genomes. Techniques have been devised to insert, delete, and modify DNA at multiple levels, ranging from a specific base pair in a specific gene to entire genes. There are a number of steps that are followed before a genetically modified organism (GMO) is created. Genetic engineers must first choose what gene they wish to insert, modify, or delete. The gene must then be isolated and incorporated, along with other genetic elements, into a suitable vector. This vector is then used to insert the gene into the host genome, creating a transgenic or edited organism.

Bacterial recombination is a type of genetic recombination in bacteria characterized by DNA transfer from one organism called donor to another organism as recipient. This process occurs in three main ways:

<span class="mw-page-title-main">Illegitimate recombination</span>

Illegitimate recombination, or nonhomologous recombination, is the process by which two unrelated double stranded segments of DNA are joined. This insertion of genetic material which is not meant to be adjacent tends to lead to genes being broken causing the protein which they encode to not be properly expressed. One of the primary pathways by which this will occur is the repair mechanism known as non-homologous end joining (NHEJ).

<span class="mw-page-title-main">Competence factor</span>

The ability of a cell to successfully incorporate exogenous DNA, or competency, is determined by competence factors. These factors consist of certain cell surface proteins and transcription factors that induce the uptake of DNA.

References

  1. 1 2 3 4 5 6 7 8 9 10 Henkin, Tina M.; Peters, Joseph E. (2020). Snyder and Champness molecular genetics of bacteria (Fifth ed.). Hoboken, NJ: John Wiley & Sons, Inc. pp. 246–260. ISBN   9781555819767.
  2. 1 2 Blokesch, Melanie (November 2016). "Natural competence for transformation". Current Biology. 26 (21): R1126–R1130. doi:10.1016/j.cub.2016.08.058.
  3. ↑ Avery, Oswald T.; MacLeod, Colin M.; McCarty, Maclyn (1 February 1944). "Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types". Journal of Experimental Medicine. 79 (2): 137–158. doi:10.1084/jem.79.2.137. PMC   2135445 . PMID   19871359.
  4. 1 2 Chen, I; Dubnau, D (2004). "DNA uptake during bacterial transformation". Nature Reviews Microbiology. 2 (3): 241–249. doi:10.1038/nrmicro844. PMID   15083159. S2CID   205499369.
  5. ↑ Johnston, Calum; Martin, Bernard; Fichant, Gwennaele; Polard, Patrice; Claverys, Jean-Pierre (March 2014). "Bacterial transformation: distribution, shared mechanisms and divergent control". Nature Reviews Microbiology. 12 (3): 181–196. doi:10.1038/nrmicro3199. PMID   24509783. S2CID   23559881.
  6. ↑ Solomon, Jonathan M.; Grossman, Alan D. (April 1996). "Who's competent and when: regulation of natural genetic competence in bacteria". Trends in Genetics. 12 (4): 150–155. doi:10.1016/0168-9525(96)10014-7. PMID   8901420.
  7. ↑ Redfield, RJ (September 1991). "sxy-1, a Haemophilus influenzae mutation causing greatly enhanced spontaneous competence". Journal of Bacteriology. 173 (18): 5612–8. doi:10.1128/jb.173.18.5612-5618.1991. PMC   208288 . PMID   1653215.
  8. ↑ Boonstra, Mirjam; Schaffer, Marc; Sousa, Joana; Morawska, Luiza; Holsappel, Siger; Hildebrandt, Petra; Sappa, Praveen Kumar; Rath, Hermann; de Jong, Anne; Lalk, Michael; Mäder, Ulrike; Völker, Uwe; Kuipers, Oscar P. (June 2020). "Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence". Environmental Microbiology. 22 (6): 2312–2328. doi:10.1111/1462-2920.15005.
  9. ↑ Findlay, WA; Redfield, RJ (2009). "Coevolution of DNA uptake sequences and bacterial proteomes". Genome Biology and Evolution. 1: 45–55. doi:10.1093/gbe/evp005. PMC   2817400 . PMID   20333176.
  10. ↑ Barton, N. H.; Charlesworth, B. (25 September 1998). "Why Sex and Recombination?". Science. 281 (5385): 1986–1990. doi:10.1126/science.281.5385.1986. PMID   9748151.
  11. ↑ Otto, S.P.; Gerstein, A.C. (1 August 2006). "Why have sex? The population genetics of sex and recombination". Biochemical Society Transactions. 34 (4): 519–522. doi:10.1042/BST0340519. PMID   16856849.
  12. ↑ Peterson, Scott; Cline, Robin T.; Tettelin, Hervé; Sharov, Vasily; Morrison, Donald A. (November 2000). "Gene Expression Analysis of the Streptococcus pneumoniae Competence Regulons by Use of DNA Microarrays". Journal of Bacteriology. 182 (21): 6192–6202. doi:10.1128/JB.182.21.6192-6202.2000. PMC   94756 . PMID   11029442.
  13. 1 2 Redfield, Rosemary J. (1988). "Is sex with dead cells ever better than no sex at all?". Genetics. 119 (1): 213–221. doi:10.1093/genetics/119.1.213. PMC   1203342 . PMID   3396864.
  14. ↑ Redfield, Rosemary J. (2001). "Do bacteria have sex?". Nature Reviews Genetics. 2 (8): 634–639. doi:10.1038/35084593. PMID   11483988. S2CID   5465846.
  15. ↑ Dubnau, D (1999). "DNA uptake in bacteria". Annual Review of Microbiology. 53 (1): 217–44. doi:10.1146/annurev.micro.53.1.217. PMID   10547691.
  16. ↑ Maughan, H (2010). "Bacterial DNA uptake sequences can accumulate by molecular drive alone". Genetics. 186 (2): 613–627. doi: 10.1534/genetics.110.119438 . PMC   2954483 . PMID   20628039.
  17. ↑ Redfield, Rosemary J.; Schrag, Matthew R; Dead, Antony M (1997). "The evolution of bacterial transformation: sex with poor relations". Genetics. 146 (1): 27–38. doi:10.1093/genetics/146.1.27. PMC   1207942 . PMID   9135998.
  18. ↑ Hoelzer, M A; Michod, R E (1 June 1991). "DNA repair and the evolution of transformation in Bacillus subtilis. III. Sex with damaged DNA". Genetics. 128 (2): 215–223. doi:10.1093/genetics/128.2.215. PMC   1204460 . PMID   1906416.
  19. ↑ Michod, Richard E.; Bernstein, Harris; Nedelcu, Aurora M. (May 2008). "Adaptive value of sex in microbial pathogens". Infection, Genetics and Evolution. 8 (3): 267–285. doi:10.1016/j.meegid.2008.01.002. PMID   18295550.
  20. ↑ Bernstein, Harris; Bernstein, Carol; Michod, Richard E. (2012). "Chapter 1 - DNA Repair as the Primary Adaptive Function of Sex in Bacteria and Eukaryotes". DNA Repair: New Research. NOVA Publishers. pp. 1–50. ISBN   978-1-62100-756-2. Archived from the original on 29 October 2013. Retrieved 13 April 2012.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.