Mycobacterium smegmatis: Difference between revisions

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===Higher order taxa===
===Higher order taxa===


Bacteria (Domain); Actinobacteria (Phylum); Actinobacteridae (Class); Actinomycetales (Order); Corynebacterineae (Suborder); Mycobacteriaceae(Family); Mycobacterium (Genus). 8.
Bacteria (Domain); Actinobacteria (Phylum); Actinobacteridae (Class); Actinomycetales (Order); Corynebacterineae (Suborder); Mycobacteriaceae (Family); Mycobacterium (Genus) (8).


===Species===  
===Species===  
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''Mycobacterium smegmatis.''
''Mycobacterium smegmatis.''


Also known by: ''Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium smegmatis. '' 7.
Also known by: ''Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium smegmatis '' (7).


==Description and significance==
==Description and significance==
''Mycobacterium smegmatis'' was first discovered in 1884 by Lustgarten. They are mostly found in the soil, marine, and freshwater environments. ''Mycobacterium smegmatis'' is classified as a saprophytic species that rarely causes disease and isn't dependent on living in an animal, unlike some pathogenic Mycobacterium.
''Mycobacterium smegmatis'' was first discovered and isolated in 1884 by Lustgarten. The name ''smegmatis'' was first given to ''Bacillus smegmatis'' by Trevisan in 1889. Lehmann and Neumann gave the species name ''smegmatis'' to ''Mycobacterium smegmatis'' in 1899.


[[Image:Myco.GIF|thumb|''Mycobacterium smegmatis on agar medium from [http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Myco.html Department of Molecular Biology by Dr. Kiesser.]]]
''Mycobacterium smegmatis'' lives in aggregate layers of cells attached to each other in a community called a biofilm. ''Mycobacterium smegmatis'' are mostly found in the soil, water, and plants. They tend mostly to exist near large bodies of water. Isolates have been discovered in 16 States, Australia, Russia, Canada, and Switzerland (1). ''Mycobacterium smegmatis'' is classified as a saprophytic species that rarely causes disease and isn't dependent on living in an animal, unlike some pathogenic Mycobacterium.  


''Mycobacterium smegmatis'' is a very useful for the research analysis of other species in the genus ''Mycobacteria'' in cell culture laboratories. There are several Mycobacterium species that are common, harmful diseases, like ''Mycobacterium leprea, Mycobacterium tuberculosis, and Mycobacterium bovis''. ''Mycobacterium smegmatis'' is so important because it is fast growing and non-pathogenic compared to these species. There are many similarities between ''Mycobacterium smegmatis'' and the much more virulent obligate pathogens that are ''Mycobacteria''. The most significant is the complementary uses of mycothiol biosynthesis of ''Mycobacterium'' for making an essential thiol that is responsible for life. If it is knocked out, the species will be terminated and a treatment will be found. 10. There is also research involved in finding drug therapies that will treat inhibit the myolic acid biosynthesis which is essential for creating the unique bacterial cell wall. 11. Currently, there are many laboratories that are culturing and isolating this species to determine the pathological course of deleterious Mycobacteria.
The bacteria will be finely wrinkled and creamy white while it is growing on accessible nutrients. When ''Mycobacterium smegmatis'' has been growing for quite some time (generally after 48 hr growth) and is abundant, the color will turn from white to a nonpigmented creamy yellow. It will also be waxy because of the high amount of unique Gram-positive cell wall coated with mycolic acids. The bacteria also ranges in textures, being seen as smooth, flat and glistening or coarsely folded or finely wrinkled (12).


Describe the appearance, habitat, etc. of the organism,  Describe how and where it was isolated.
''Mycobacterium smegmatis'' is very useful for the research analysis of other species in the genus ''Mycobacteria'' in cell culture laboratories. There are several Mycobacterial species that are common, harmful diseases, like ''Mycobacterium leprea, Mycobacterium tuberculosis, and Mycobacterium bovis''. ''Mycobacterium smegmatis'' is so important because it is fast growing and non-pathogenic compared to these species. There are many similarities between ''Mycobacterium smegmatis'' and the much more virulent obligate pathogens that are ''Mycobacteria''. The most significant is the complementary uses of mycothiol biosynthesis of ''Mycobacterium'' for making an essential thiol that is responsible for life. If it is knocked out, the species will be terminated and a treatment will be found (10). There is also research involved in finding drug therapies that will inhibit the myolic acid biosynthesis which is essential for creating the unique bacterial cell wall (11). Currently, there are many laboratories that are culturing and isolating this species to determine the pathological course of deleterious ''Mycobacteria''.
Include a picture or two (with sources) if you can find them.


==Genome structure==
==Genome structure==
[[Image:Ncgraph.png|thumb|500px|left| A cartoon of the ''Mycobacterium smegmatis'' gene.  From [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=20087 NCBI Entrez Genome Website.]]]
The genome of ''Mycobacterium smegmatis'' is 6,988,209 nucleotides long. It has a 67% guanine cytosine content and a 33% adenosine thymine content, and is therefore classified as a high GC content gram-positive bacteria (discussed below). 90% of the genome (6716/6938 genes) represents coding regions that encode for 6716 proteins. The 6938 genes are composed circularly with an absence of any plasmids. ''Mycobacterium smegmatis'' is a slow growing bacteria which contains one copy of the ribosomal RNA genes unlike fast growing bacteria (e.g. ''Escherichia coli'') which has two copies of the rRNA genes. ''Mycobacterium smegmatis'' doesn't need so many copies of the genes because it doesn't require the high production of proteins when it is growing slow, while ''Escherichia coli'' does. The genome was sequenced in November 29, 2006 by the J. Craig Venter Institute (9).
 
The genome is 6,988,209 nucleotides long. It has a 67% GC content and a 33% AT content, and is therefore classified as a high GC content gram positive bacteria (discussed below). 90% of the genome (6716/6938 genes) represents coding regions that encode for 6716 proteins. The 6938 genes that are composed circularly with an absence of any plasmids. ''Mycobacterium smegmatis'' is a slow growing bacteria which contains one copy of the ribosomal RNA genes unlike fast growing bacteria (Eg. ''Escherichia coli'') which has two copies of the rRNA genes. ''Mycobacterium smegmatis'' doesn't need so many copies of the genes because it doesn't require the high production of proteins when it is growing slow, while ''Escherichia coli'' does. The genome was sequenced in November 29, 2006 by the J. Craig Venter Institute. 9.
 
[[Image:Ncgraph2.png|thumb|350px|left| A map of the genes from the first 10,000 bp in the genome. From [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=20087 NCBI Entrez Genome Website.]]]


==Cell structure and metabolism==
==Cell structure and metabolism==
''Mycobacterium smegmatis'' is a Gram-positive bacteria, characterized by an inner cell membrane and a thick cell wall. The Gram-positive bacteria is further classified as one with a high GC content and therefore a low AT content. This quality is used as a rude measure of similarity of different species of bacteria. Although this bacteria is Gram-positive, its cell wall contains mycolic acids, long, branched fatty acids that are normally present in Acid-fast bacteria. The acids prevent proper gram staining that would normally identify the cell as a gram positive cell because they create a waxy coating so the crystal violet has difficulty entering the cell, therefore making it seem gram negative.
''Mycobacterium smegmatis'' is a Gram-positive bacteria, characterized by an inner cell membrane and a thick cell wall. The Gram-positive bacteria is further classified as one with a high GC content and therefore a low AT content. This quality is used as a crude measure of similarity of different species of bacteria. Although this bacteria is Gram-positive, it has some unique qualities that are divergent from most Gram-positive bacteria. Its cell wall contains mycolic acids, long, branched fatty acids that are normally present in scid-fast bacteria. The acids prevent proper gram staining that would normally identify the cell as a gram positive cell because they create a waxy coating so the crystal violet has difficulty entering the cell, therefore making it seem gram-negative.
The cell wall is also abnormal because it is irregularly thick for a gram positive bacteria and its hydrophobicity reduces dessication. This feature in addition to its slow cell growth attribute to ''Mycobacterium smegmatis''' low response to antibiotics.
The cell wall is also abnormal because it is irregularly thick for a gram-positive bacteria and its hydrophobicity reduces desiccation. This feature in addition to its slow cell growth (in comparison to most other bacteria) attribute to ''Mycobacterium smegmatis''' low response to antibiotics. Although ''Mycobacterium smegmatis'' contains the similar structural features of ''Mycobacterium tuberculosis'', the former grows much quicker in comparison to the latter (12).


Although it contains the similar structural features of ''Mycobacterium Tuberculosis'', it grows much quicker in comparison. ''Mycobacterium smegmatis'' is an aerobic organism. Small amounts of ''Mycobacterium smegmatis'' may also survive on chemolithoautotrophic growth. They would use carbon dioxide and hydrogen gas as its inorganic fuel source. It also requires a unique fatty acid biosynthesis to produce the mycolic acids that are present on the cell wall.
''Mycobacterium smegmatis'' is an aerobic organism. ''Mycobacerium smegmatis'' may donate its final electrons in aerobic respiration to oxygen using one of three terminal oxidases. In aerobic respiration, the bacteria undergo oxidative phosphorylation to yield the highest amount of energy. Since ''Mycobacteria'' are obligate aerobes, oxygen is required for aerobic respiration. ''Mycobacterium smegmatis'' doesn't undergo anaerobic respiration, however certain virulent ''Mycobacteria'' undergo anaerobic respiration only during infection. ''Mycobacterium smegmatis'' may survive on chemolithotrophic growth on carbon monoxide as its inorganic carbon source during aerobic respiration. The bacteria may also use methanol for its sole source carbon and energy. In addition, ''Mycobacterium smegmatis'' requires a unique fatty acid biosynthesis to produce the mycolic acids that are present on the cell wall. ''Mycobacterium smegmatis'' has no motility and no formation of endospores (3, 13, 14).


==Ecology==
==Ecology==
''Mycobacterium smegmatis'' lives in aggregate layers of cells attached to each other in a community called a biofilm. may live in soil and degrade organic materials, including sterols. The bacteria lives in water, and tends to exist near large bodies of water.
Biofilms of ''Mycobacterium smegmatis'' may use stigmasterol as a carbon source from plants. The bacteria will metabolize the compound to a potent androgen, androstenedione. If ''Mycobacterium smegmatis'' is around a large body of water, which is where it usually exists, then the bacteria will secrete androstenedione. The androgen in the water causes female mosquito fish to form male anatomical sex organs (15). Not much else could be found about the contribution to the environment.  
 
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.


==Pathology==
==Pathology==


This organism is classified as saprophytic and therefore extremely unpathogenic. ''Mycobacterium smegmatis'' doesn't normally reside in any animals, and doesn't cause dangerous or even any infections.  There are no threats as it is very safe. However other species under this genus are pathogenic. Obligate pathogens such as ''Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium leprea'' are highly pathogenic in animals. These species can cause tuberculosis and leprosy. There is also the classification of potential pathogens in this genus, such as ''Mycobacterium avium''.
This organism is classified as saprophytic and therefore relatively safe. ''Mycobacterium smegmatis'' doesn't normally reside in any animals, and doesn't cause dangerous or even any infections.  There have only been a few threats, which have seem to come out in only extreme cases, however there hasn't been any documented virulence of ''Mycobacterium smegmatis'' in over 15 years. There are many other species under this genus are pathogenic. Obligate pathogens such as ''Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium leprea'' are highly pathogenic in animals. These species can cause tuberculosis and leprosy, debilitating diseases that may lead to death or disfigurement. These pathogens can only survive inside the host organism. There is also the classification of potential pathogens in this genus, such as ''Mycobacterium avium'', which may survive outside of the host environment and cause virulence once it is contracted by the host.


However, there has been 1 case where the bacteria has killed a human after infection. In this case, an Italian child was infected by ''Mycobacterium smegmatis'' and died at the age of 8. After genetic analysis, it was determined that four nucleotides were inserted, causing a frameshift and a nonsense mutation. The stop codon allowed for a premature stop of translation. Although this showed potential pathogenic properties of ''Mycobacterium smegmatis'', this case required that the child have two mutant alleles in his genome for the bacteria to be particularly virulent. Therefore in most cases, it is generally safe. 5.
However, there has been 1 case where the bacteria has killed a human after infection. In this case, an Italian child was infected by ''Mycobacterium smegmatis'' and died at the age of 8. After genetic analysis of the child, it was determined that four nucleotides were inserted, causing a frameshift and a nonsense mutation. The stop codon allowed for a premature stop of translation and essential proteins weren't made. Although this showed potential pathogenic properties of ''Mycobacterium smegmatis'', this case required that the child have two mutant alleles in his genome for the bacteria to be particularly virulent. Therefore in most cases, ''Mycobacterium smegmatis'' is generally safe and not pathogenic (5).


==Application to Biotechnology==
==Application to Biotechnology==
''Mycobacterium smegmatis'' has been used to produce Xylitol. Xylitol is an important sugar that is used as a substitute for commercial dietary sugars to prevent tooth decay. It is also a plaque reducer. It is also absorbed more slowly in the bloodstream, so it prevents the negative affects of high blood sugar levels. This is used as a dietary alternative for diabetics. It also has potential treatments for osteoporosis and ear and upper respiratory infections. The D-xylulose sugar produced by ''Mycobacterium smegmatis'' is combined with the D-xylose sugar produced by D-xylose isomerase of immobilized ''Mycobacterium smegmatis'' to produce the beneficial Xylitol. 6.
''Mycobacterium smegmatis'' has been used to produce Xylitol. Xylitol is an important sugar that is used as a substitute for commercial dietary sugars to prevent tooth decay and reduce plaque. It is also absorbed more slowly in the bloodstream, so it prevents the negative affects of high blood sugar levels. This is used as a dietary alternative for diabetics. It also has potential treatments for osteoporosis and ear and upper respiratory infections. The D-xylulose sugar produced by ''Mycobacterium smegmatis'' is combined with the D-xylose sugar produced by D-xylose isomerase of immobilized ''Mycobacterium smegmatis'' to produce the beneficial Xylitol (6).


''Mycobacterium smegmatis'' is also used to transform L-ribulose into L-arabinose with the enzyme L-arabinose isomerase. ''Mycobacterium smegmatis''' produces L-arabinose during carbohydrate metabolism. L-arabinose is used by biotech companies to produce chiral drugs. L-arabinose is also used as a component for many tissue culture medium. It is also used by food producers for the Maillard reaction to make bread, beer, dried or condensed milk, etc. 6.
''Mycobacterium smegmatis'' is also used to transform L-ribulose into L-arabinose with the enzyme L-arabinose isomerase. ''Mycobacterium smegmatis'' produces L-arabinose during carbohydrate metabolism. L-arabinose is used by biotech companies to produce chiral drugs. Researchers use L-arabinose as a component for many tissue culture medium. It is also used by food producers for the Maillard reaction to make bread, beer, dried or condensed milk, etc. (6).


==Current Research==
==Current Research==
Dr. Fahey's lab at UCSD studies the methods of mycothiol biosynthesis that produces the thiols that are needed for ''Mycobacterium'' to live and grow. The lab is trying to determine the missing and unknown enzymes and substrates that are present in the biosynthesis and if they are essential. There are currently three steps that have been determined by this lab. They are trying to determine the unknown substrate that is converted to GlcNAc-Ins from the enzyme MshA. From 3 more known steps using MshB, MshC, and MshD, the necessary mycothiol is produced. The Fahey lab aims to determine the unknown substrate to determine the full mycothiol biosynthesis pathway, and to determine some inhibitors of this pathway to prevent ''Mycobacterium smegmatis'' growth, which can also translate to treatments for ''Mycobacterium tuberculosis''. 2
Dr. Fahey's lab at UCSD studies the methods of mycothiol biosynthesis that produces thiols necessary for ''Mycobacterium'' to live and grow. The lab is trying to determine the missing and unknown enzymes and substrates that are present in the biosynthesis pathway and if they are essential. There are currently three steps that have been determined by this lab. They are trying to determine the unknown substrate that is converted to GlcNAc-Ins from the enzyme MshA. From 3 more known steps using MshB, MshC, and MshD, the necessary mycothiol is produced. The Fahey lab aims to determine the unknown substrate to determine the full mycothiol biosynthesis pathway, and to determine some inhibitors of this pathway to prevent ''Mycobacterium smegmatis'' growth. Since ''Mycobacterium smegmatis'' has the same mechanism to create its cell wall as ''Mycobacterium tuberculosis'', this can translate into treatments tuberculosis. 2


''Mycobacterium smegmatis'' uses a terminal oxidase to donate electrons to the final electron acceptor oxygen in oxidative phosphorylation during aerobic respiration. These terminal oxidases have been identified as using both a cytochrome c aa3 type oxidase and a quinol bd type oxidase. When bd type oxidase gene is knocked out to only allow for the cytochrome c aa3 type oxidase to function, the latter didn't attain normal levels of expression of the oxidase. In addition, the oxidase concentration for the knockout didn't reduce during log phase, while the wild type(without the knockout) had decreased oxidase concentration. 3
''Mycobacterium smegmatis'' uses a terminal oxidase to donate electrons to the final electron acceptor oxygen in oxidative phosphorylation during aerobic respiration. These terminal oxidases have been identified as using both a cytochrome c aa3 type oxidase and a quinol bd type oxidase. When bd type oxidase gene is knocked out so cytochrome c aa3 type oxidase is the only functional oxidase, the latter didn't attain normal levels of expression of the oxidase. In addition, the oxidase concentration for the knockout didn't reduce during log phase, while the wild type (without the knockout) had decreased oxidase concentration (3).


''Mycobacteria smegmatis'' is also dependent on the import of free inorganic phosphate molecules. Genes that regulate this import are often two component regulatory systems that are composed of histidine kinase and a DNA-binding response regulator. One of these regulators discovered by Dr. Glover is senX3-regX3 2CR. SenX3 acts as a phosphotase and a phosphate donor for regX3. A phosphorylated regX3 will activate phosphate acquisition. RegX3-P is bound to the promoter regions and activates the transcription of senX3, phoA, pstS genes that activate inorganic phosphate import. Therefore this group has determined that the senX3-regX3 2CR system is responsible for regulating this pathway. 4
''Mycobacteria smegmatis'' is also dependent on the import of free inorganic phosphate molecules. Genes that regulate this import are often two component regulatory systems that are composed of a histidine kinase and a DNA-binding response regulator. One of these regulators discovered by Dr. Glover is senX3-regX3 2CR. SenX3 acts as a phosphatase and a phosphate donor for regX3. A phosphorylated regX3 will activate phosphate acquisition. RegX3-P is bound to the promoter regions and activates the transcription of senX3, phoA, pstS genes that activate inorganic phosphate import. Therefore this group has determined that the senX3-regX3 2CR system is responsible for regulating this pathway (4).


==References==
==References==
1. Dastur, A., Kumar, P., Ramesh, S., Vasanthakrishna, M., Varshney, U. "Analysis of the initiator tRNA genes from a slow- and a fast-growing Mycobacterium" Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12209262&dopt=Abstract
1. Brown-Elliott, B., Wallace, R. "Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria". Clinical Microbiology Reviews. 2002. Volume 15. p. 716–746. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12364376


2. Newton, G., Ta, P., Bzymek, K., Fahey, R. "Biochemisrty of the Initial Steps of Mycothiol Biosynthesis" Journal of Biological Chemistry. 2006. Volume 281. p. 33910-20. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16940050&query_hl=9&itool=pubmed_docsum
2. Newton, G., Ta, P., Bzymek, K., Fahey, R. "Biochemisrty of the Initial Steps of Mycothiol Biosynthesis" Journal of Biological Chemistry. 2006. Volume 281. p. 33910-20. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16940050&query_hl=9&itool=pubmed_docsum
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5. Branca, A., Baglioni, C. "Evidence that types I and II interferons have different receptors." Nature. 1981. Volume 294: p. 768-770. http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=107470
5. Branca, A., Baglioni, C. "Evidence that types I and II interferons have different receptors." Nature. 1981. Volume 294: p. 768-770. http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=107470


6. Ahmed, Z. "Production of natural and rare pentoses using microorganisms and their enzymes." Electronic Journal of Biotechnology. 2001. Volume 4. Number 2.
6. Ahmed, Z. "Production of natural and rare pentoses using microorganisms and their enzymes." Electronic Journal of Biotechnology. 2001. Volume 4. Number 2. http://www.ejbiotechnology.info/content/vol4/issue2/full/7/bip/index.html


7. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1772&lvl=3&lin=f&keep=1&srchmode=1&unlock
7. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1772&lvl=3&lin=f&keep=1&srchmode=1&unlock
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11. Schroeder, E., de Souza, N., Santos, D., Blanchard, J., Basso, L. "Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis." Curr Pharm Biotechnol. 2002. Volume 3. p. 197-225.  http://www.ingentaconnect.com/content/ben/cpb/2002/00000003/00000003/art00002?token=004816d0ad50b6726e2d2954496f642f466f256720297d7625627b507b5f5f316a6f3874
11. Schroeder, E., de Souza, N., Santos, D., Blanchard, J., Basso, L. "Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis." Curr Pharm Biotechnol. 2002. Volume 3. p. 197-225.  http://www.ingentaconnect.com/content/ben/cpb/2002/00000003/00000003/art00002?token=004816d0ad50b6726e2d2954496f642f466f256720297d7625627b507b5f5f316a6f3874
12. Gordon, R., Smith, M. "RAPIDLY GROWING, ACID FAST BACTERIA I. Species' Descriptions of Mycobacterium phlei Lehmann and Neumann and Mycobacterium smegmatis (Trevisan) Lehmann and Neumann".
Journal of Bacteriology. 1953. Volume 66. p. 41-48. http://www.pubmedcentral.nih.gov/pagerender.fcgi?artid=357089&pageindex=1
13. Weber, I., Fritz, C., Ruttkowski, S., Kreft, A., Bange, F. "Anaerobic nitrate reductase (narGHJI) activity of Mycobacterium bovis BCG in vitro and its contribution to virulence in immunodeficient mice" Molecular microbiology. 2000. Volume 35. p. 1017. http://www.blackwell-synergy.com/doi/abs/10.1046/j.1365-2958.2000.01794.x
14. Park, S. Hwang, E., Park, H., Kim, J., Heo, J., Lee, K., Song, T., Kim, E., Ro, T., Kim, S., Kim, Y. "Growth of Mycobacteria on Carbon Monoxide and Methanol". Journal of Bacteriology. 2001. Volume 185. p. 142–147. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=141938
15. McLachlan, J. "Environmental Signaling: What Embryos and Evolution Teach Us About Endocrine Disrupting Chemical." Endocrine Reviews. Volume 22. p. 319-344. http://edrv.endojournals.org/cgi/content/full/22/3/319


Edited by Benjamin Yip, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
Edited by Benjamin Yip, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
KMG

Latest revision as of 18:58, 22 April 2011

This is a curated page. Report corrections to Microbewiki.

A Microbial Biorealm page on the genus Mycobacterium smegmatis

Classification

Higher order taxa

Bacteria (Domain); Actinobacteria (Phylum); Actinobacteridae (Class); Actinomycetales (Order); Corynebacterineae (Suborder); Mycobacteriaceae (Family); Mycobacterium (Genus) (8).

Species

Mycobacterium smegmatis.

Also known by: Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium paratuberculosis smegmatis, Bacterium smegmatis, Bacillus smegmatis, Mycobacterium smegmatis (7).

Description and significance

Mycobacterium smegmatis was first discovered and isolated in 1884 by Lustgarten. The name smegmatis was first given to Bacillus smegmatis by Trevisan in 1889. Lehmann and Neumann gave the species name smegmatis to Mycobacterium smegmatis in 1899.

Mycobacterium smegmatis lives in aggregate layers of cells attached to each other in a community called a biofilm. Mycobacterium smegmatis are mostly found in the soil, water, and plants. They tend mostly to exist near large bodies of water. Isolates have been discovered in 16 States, Australia, Russia, Canada, and Switzerland (1). Mycobacterium smegmatis is classified as a saprophytic species that rarely causes disease and isn't dependent on living in an animal, unlike some pathogenic Mycobacterium.

The bacteria will be finely wrinkled and creamy white while it is growing on accessible nutrients. When Mycobacterium smegmatis has been growing for quite some time (generally after 48 hr growth) and is abundant, the color will turn from white to a nonpigmented creamy yellow. It will also be waxy because of the high amount of unique Gram-positive cell wall coated with mycolic acids. The bacteria also ranges in textures, being seen as smooth, flat and glistening or coarsely folded or finely wrinkled (12).

Mycobacterium smegmatis is very useful for the research analysis of other species in the genus Mycobacteria in cell culture laboratories. There are several Mycobacterial species that are common, harmful diseases, like Mycobacterium leprea, Mycobacterium tuberculosis, and Mycobacterium bovis. Mycobacterium smegmatis is so important because it is fast growing and non-pathogenic compared to these species. There are many similarities between Mycobacterium smegmatis and the much more virulent obligate pathogens that are Mycobacteria. The most significant is the complementary uses of mycothiol biosynthesis of Mycobacterium for making an essential thiol that is responsible for life. If it is knocked out, the species will be terminated and a treatment will be found (10). There is also research involved in finding drug therapies that will inhibit the myolic acid biosynthesis which is essential for creating the unique bacterial cell wall (11). Currently, there are many laboratories that are culturing and isolating this species to determine the pathological course of deleterious Mycobacteria.

Genome structure

The genome of Mycobacterium smegmatis is 6,988,209 nucleotides long. It has a 67% guanine cytosine content and a 33% adenosine thymine content, and is therefore classified as a high GC content gram-positive bacteria (discussed below). 90% of the genome (6716/6938 genes) represents coding regions that encode for 6716 proteins. The 6938 genes are composed circularly with an absence of any plasmids. Mycobacterium smegmatis is a slow growing bacteria which contains one copy of the ribosomal RNA genes unlike fast growing bacteria (e.g. Escherichia coli) which has two copies of the rRNA genes. Mycobacterium smegmatis doesn't need so many copies of the genes because it doesn't require the high production of proteins when it is growing slow, while Escherichia coli does. The genome was sequenced in November 29, 2006 by the J. Craig Venter Institute (9).

Cell structure and metabolism

Mycobacterium smegmatis is a Gram-positive bacteria, characterized by an inner cell membrane and a thick cell wall. The Gram-positive bacteria is further classified as one with a high GC content and therefore a low AT content. This quality is used as a crude measure of similarity of different species of bacteria. Although this bacteria is Gram-positive, it has some unique qualities that are divergent from most Gram-positive bacteria. Its cell wall contains mycolic acids, long, branched fatty acids that are normally present in scid-fast bacteria. The acids prevent proper gram staining that would normally identify the cell as a gram positive cell because they create a waxy coating so the crystal violet has difficulty entering the cell, therefore making it seem gram-negative. The cell wall is also abnormal because it is irregularly thick for a gram-positive bacteria and its hydrophobicity reduces desiccation. This feature in addition to its slow cell growth (in comparison to most other bacteria) attribute to Mycobacterium smegmatis' low response to antibiotics. Although Mycobacterium smegmatis contains the similar structural features of Mycobacterium tuberculosis, the former grows much quicker in comparison to the latter (12).

Mycobacterium smegmatis is an aerobic organism. Mycobacerium smegmatis may donate its final electrons in aerobic respiration to oxygen using one of three terminal oxidases. In aerobic respiration, the bacteria undergo oxidative phosphorylation to yield the highest amount of energy. Since Mycobacteria are obligate aerobes, oxygen is required for aerobic respiration. Mycobacterium smegmatis doesn't undergo anaerobic respiration, however certain virulent Mycobacteria undergo anaerobic respiration only during infection. Mycobacterium smegmatis may survive on chemolithotrophic growth on carbon monoxide as its inorganic carbon source during aerobic respiration. The bacteria may also use methanol for its sole source carbon and energy. In addition, Mycobacterium smegmatis requires a unique fatty acid biosynthesis to produce the mycolic acids that are present on the cell wall. Mycobacterium smegmatis has no motility and no formation of endospores (3, 13, 14).

Ecology

Biofilms of Mycobacterium smegmatis may use stigmasterol as a carbon source from plants. The bacteria will metabolize the compound to a potent androgen, androstenedione. If Mycobacterium smegmatis is around a large body of water, which is where it usually exists, then the bacteria will secrete androstenedione. The androgen in the water causes female mosquito fish to form male anatomical sex organs (15). Not much else could be found about the contribution to the environment.

Pathology

This organism is classified as saprophytic and therefore relatively safe. Mycobacterium smegmatis doesn't normally reside in any animals, and doesn't cause dangerous or even any infections. There have only been a few threats, which have seem to come out in only extreme cases, however there hasn't been any documented virulence of Mycobacterium smegmatis in over 15 years. There are many other species under this genus are pathogenic. Obligate pathogens such as Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium leprea are highly pathogenic in animals. These species can cause tuberculosis and leprosy, debilitating diseases that may lead to death or disfigurement. These pathogens can only survive inside the host organism. There is also the classification of potential pathogens in this genus, such as Mycobacterium avium, which may survive outside of the host environment and cause virulence once it is contracted by the host.

However, there has been 1 case where the bacteria has killed a human after infection. In this case, an Italian child was infected by Mycobacterium smegmatis and died at the age of 8. After genetic analysis of the child, it was determined that four nucleotides were inserted, causing a frameshift and a nonsense mutation. The stop codon allowed for a premature stop of translation and essential proteins weren't made. Although this showed potential pathogenic properties of Mycobacterium smegmatis, this case required that the child have two mutant alleles in his genome for the bacteria to be particularly virulent. Therefore in most cases, Mycobacterium smegmatis is generally safe and not pathogenic (5).

Application to Biotechnology

Mycobacterium smegmatis has been used to produce Xylitol. Xylitol is an important sugar that is used as a substitute for commercial dietary sugars to prevent tooth decay and reduce plaque. It is also absorbed more slowly in the bloodstream, so it prevents the negative affects of high blood sugar levels. This is used as a dietary alternative for diabetics. It also has potential treatments for osteoporosis and ear and upper respiratory infections. The D-xylulose sugar produced by Mycobacterium smegmatis is combined with the D-xylose sugar produced by D-xylose isomerase of immobilized Mycobacterium smegmatis to produce the beneficial Xylitol (6).

Mycobacterium smegmatis is also used to transform L-ribulose into L-arabinose with the enzyme L-arabinose isomerase. Mycobacterium smegmatis produces L-arabinose during carbohydrate metabolism. L-arabinose is used by biotech companies to produce chiral drugs. Researchers use L-arabinose as a component for many tissue culture medium. It is also used by food producers for the Maillard reaction to make bread, beer, dried or condensed milk, etc. (6).

Current Research

Dr. Fahey's lab at UCSD studies the methods of mycothiol biosynthesis that produces thiols necessary for Mycobacterium to live and grow. The lab is trying to determine the missing and unknown enzymes and substrates that are present in the biosynthesis pathway and if they are essential. There are currently three steps that have been determined by this lab. They are trying to determine the unknown substrate that is converted to GlcNAc-Ins from the enzyme MshA. From 3 more known steps using MshB, MshC, and MshD, the necessary mycothiol is produced. The Fahey lab aims to determine the unknown substrate to determine the full mycothiol biosynthesis pathway, and to determine some inhibitors of this pathway to prevent Mycobacterium smegmatis growth. Since Mycobacterium smegmatis has the same mechanism to create its cell wall as Mycobacterium tuberculosis, this can translate into treatments tuberculosis. 2

Mycobacterium smegmatis uses a terminal oxidase to donate electrons to the final electron acceptor oxygen in oxidative phosphorylation during aerobic respiration. These terminal oxidases have been identified as using both a cytochrome c aa3 type oxidase and a quinol bd type oxidase. When bd type oxidase gene is knocked out so cytochrome c aa3 type oxidase is the only functional oxidase, the latter didn't attain normal levels of expression of the oxidase. In addition, the oxidase concentration for the knockout didn't reduce during log phase, while the wild type (without the knockout) had decreased oxidase concentration (3).

Mycobacteria smegmatis is also dependent on the import of free inorganic phosphate molecules. Genes that regulate this import are often two component regulatory systems that are composed of a histidine kinase and a DNA-binding response regulator. One of these regulators discovered by Dr. Glover is senX3-regX3 2CR. SenX3 acts as a phosphatase and a phosphate donor for regX3. A phosphorylated regX3 will activate phosphate acquisition. RegX3-P is bound to the promoter regions and activates the transcription of senX3, phoA, pstS genes that activate inorganic phosphate import. Therefore this group has determined that the senX3-regX3 2CR system is responsible for regulating this pathway (4).

References

1. Brown-Elliott, B., Wallace, R. "Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria". Clinical Microbiology Reviews. 2002. Volume 15. p. 716–746. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12364376

2. Newton, G., Ta, P., Bzymek, K., Fahey, R. "Biochemisrty of the Initial Steps of Mycothiol Biosynthesis" Journal of Biological Chemistry. 2006. Volume 281. p. 33910-20. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16940050&query_hl=9&itool=pubmed_docsum

3. Megehee, J., Lundrigan, M. "Temporal expression of Mycobacterium smegmatis respiratory terminal oxidases" Canadian Journal of Microbiology. 2007. Volume 53. p. 459-6. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17538658&query_hl=5&itool=pubmed_docsum

4. Glover, R., Kriakov, J., Garforth, S., Baughn, A., Jacobs, W. "The Two-Component Regulatory System senX3-regX3 Regulates Phosphate-Dependent Gene Expression in Mycobacterium smegmatis." Journal of Bacteriology. 2007. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17526710&query_hl=5&itool=pubmed_docsum

5. Branca, A., Baglioni, C. "Evidence that types I and II interferons have different receptors." Nature. 1981. Volume 294: p. 768-770. http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=107470

6. Ahmed, Z. "Production of natural and rare pentoses using microorganisms and their enzymes." Electronic Journal of Biotechnology. 2001. Volume 4. Number 2. http://www.ejbiotechnology.info/content/vol4/issue2/full/7/bip/index.html

7. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1772&lvl=3&lin=f&keep=1&srchmode=1&unlock

8. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1772&lvl=3&lin=f&keep=1&srchmode=1&unlock

9. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=20087

10. Newton, G., Fahey, R. "Mycothiol biochemistry." Arch Microbiol. 2002. Volume 178. p. 388-94. http://www.springerlink.com/content/0jvtmpat4863q0vk/

11. Schroeder, E., de Souza, N., Santos, D., Blanchard, J., Basso, L. "Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis." Curr Pharm Biotechnol. 2002. Volume 3. p. 197-225. http://www.ingentaconnect.com/content/ben/cpb/2002/00000003/00000003/art00002?token=004816d0ad50b6726e2d2954496f642f466f256720297d7625627b507b5f5f316a6f3874

12. Gordon, R., Smith, M. "RAPIDLY GROWING, ACID FAST BACTERIA I. Species' Descriptions of Mycobacterium phlei Lehmann and Neumann and Mycobacterium smegmatis (Trevisan) Lehmann and Neumann". Journal of Bacteriology. 1953. Volume 66. p. 41-48. http://www.pubmedcentral.nih.gov/pagerender.fcgi?artid=357089&pageindex=1

13. Weber, I., Fritz, C., Ruttkowski, S., Kreft, A., Bange, F. "Anaerobic nitrate reductase (narGHJI) activity of Mycobacterium bovis BCG in vitro and its contribution to virulence in immunodeficient mice" Molecular microbiology. 2000. Volume 35. p. 1017. http://www.blackwell-synergy.com/doi/abs/10.1046/j.1365-2958.2000.01794.x

14. Park, S. Hwang, E., Park, H., Kim, J., Heo, J., Lee, K., Song, T., Kim, E., Ro, T., Kim, S., Kim, Y. "Growth of Mycobacteria on Carbon Monoxide and Methanol". Journal of Bacteriology. 2001. Volume 185. p. 142–147. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=141938

15. McLachlan, J. "Environmental Signaling: What Embryos and Evolution Teach Us About Endocrine Disrupting Chemical." Endocrine Reviews. Volume 22. p. 319-344. http://edrv.endojournals.org/cgi/content/full/22/3/319

Edited by Benjamin Yip, student of Rachel Larsen and Kit Pogliano

KMG

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