Mesoplasma florum: Difference between revisions
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==Classification== | ==Classification== | ||
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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]''' | '''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]''' | ||
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==Description and significance== | ==Description and significance== | ||
''Mesoplasma florum'' is a ''Mycoplasma'' species, which come from the bacteria Mollicutes. Mollicutes do not have a cell wall and are parasitic to humans, animals, and plants. ''Mycoplasma'' are characteristically small, as well as self-replicating. Although ''Mesoplasma florum'' are a species of ''Mycoplasma,'' ''Mesoplasma florum'' are not parasitic and are non-motile, unlike ''Mycoplasma.'' Like ''Mycoplasma,'' ''Mesoplasma florum'' are also have a very small genome size (smaller than 1Mb). (1) ''Mesoplasma florum'' was isolated from the flower of a lemon tree, and is therefore thought to be associated with plant insect vectors. (5) | ''Mesoplasma florum'' is a ''Mycoplasma'' species, which come from the bacteria ''Mollicutes''. ''Mollicutes'' do not have a cell wall and are parasitic to humans, animals, and plants. ''Mycoplasma'' are characteristically small, as well as self-replicating. Although ''Mesoplasma florum'' are a species of ''Mycoplasma,'' ''Mesoplasma florum'' are not parasitic and are non-motile, unlike ''Mycoplasma.'' Like ''Mycoplasma,'' ''Mesoplasma florum'' are also have a very small genome size (smaller than 1Mb). (1) ''Mesoplasma florum'' was isolated from the flower of a lemon tree, and is therefore thought to be associated with plant insect vectors. (5) | ||
Gene sequencing of ''Mesoplasma florum'' is important because it is the smallest self-replicating organism, ''Mycoplasma,'' and therefore, is itself very small. Furthermore, ''Mecoplasma florum'' is non-motile, so it is used to study and identify genes that are linked to motility.(1) Researchers working with ''Mesoplasma florum'' can use this species to understand why it has evolved to be non-motile even though ''Mycoplasma'' are motile, as well as why it has evolved to become non-parasitc. This shows us that ''Mycoplasma'' are highly evolving, and therefore are highly successful, therefore, gene sequencing of ''Mesoplasma florum'' is important because it is important in learning as to why ''Mesoplasma florum'' have evolved the way that it has. (2) As a result of their small genomes, they do not have a lot of metabolic ability. (2) They can easily adapt to their environment, even if that environment is changing. (1) This is important because ''Mesoplasma florum,'' as well as all species of ''Mycoplasma,'' uptake their nutrients from their environment. (3) Therefore, it is important to understand why this organism can thrive by uptaking nutrients which are continually changing. | Gene sequencing of ''Mesoplasma florum'' is important because it is the smallest self-replicating organism, ''Mycoplasma,'' and therefore, is itself very small. Furthermore, ''Mecoplasma florum'' is non-motile, so it is used to study and identify genes that are linked to motility.(1) Researchers working with ''Mesoplasma florum'' can use this species to understand why it has evolved to be non-motile even though ''Mycoplasma'' are motile, as well as why it has evolved to become non-parasitc. This shows us that ''Mycoplasma'' are highly evolving, and therefore are highly successful, therefore, gene sequencing of ''Mesoplasma florum'' is important because it is important in learning as to why ''Mesoplasma florum'' have evolved the way that it has. (2) As a result of their small genomes, they do not have a lot of metabolic ability. (2) They can easily adapt to their environment, even if that environment is changing. (1) This is important because ''Mesoplasma florum,'' as well as all species of ''Mycoplasma,'' uptake their nutrients from their environment. (3) Therefore, it is important to understand why this organism can thrive by uptaking nutrients which are continually changing. | ||
''Mesoplasma florum'' is not closely related to ''Mycoplasma genitalium'' and ''Mycoplasma pneumoniae.'' Although sterol is required in media for growth of Mollicutes, ''Mesoplasma florum'' does not require sterol. (1) | ''Mesoplasma florum'' is not closely related to ''Mycoplasma genitalium'' and ''Mycoplasma pneumoniae.'' Although sterol is required in media for growth of ''Mollicutes'', ''Mesoplasma florum'' does not require sterol. (1) | ||
==Genome structure== | ==Genome structure== | ||
''M. florum'' has a uniquely small genome size (smaller than 1Mb), due to its evolution from Mycoplasmas, which evolved from Gram-positive bacteria by reducing genome size many times. ''Mesoplasma florum'' has another unique genome characteristic in that in Mycoplasmas, the stop codon, UGA, has been changed to be translated as tryptophan. (1) (See Current research for further information). | ''M. florum'' has a uniquely small genome size (smaller than 1Mb), due to its evolution from ''Mycoplasmas'', which evolved from Gram-positive bacteria by reducing genome size many times. ''Mesoplasma florum'' has another unique genome characteristic in that in ''Mycoplasmas'', the stop codon, UGA, has been changed to be translated as tryptophan. (1) (See Current research for further information). | ||
Currently, genome sequencing for ''M. florum'' is being performed by Tom Knight, Senior Research Scientist at the MIT Artificial Intelligence Laboratory and the MIT Electrical Engineering and Computer Science Department, and the Broad Institute of MIT and Harvard. The ''Mesoplasma florum'' project will eventually yield gene discovery and further analysis of this species. The ''M. florum'' genome has been fully annotated. The method employed for sequencing the genome was Whole Genome Shotgun, where DNA is isolated from ''M. florum'' and cut into smaller fragments. These DNA fragments are then inserted into and vector and cloned, and both ends of the DNA fragments are sequenced, which produces paired reads. The paired reads are used to identify contigs, (contiguous stretches of sequence) which are ordered into supercontigs. (1) | Currently, genome sequencing for ''M. florum'' is being performed by Tom Knight, Senior Research Scientist at the MIT Artificial Intelligence Laboratory and the MIT Electrical Engineering and Computer Science Department, and the Broad Institute of MIT and Harvard. The ''Mesoplasma florum'' project will eventually yield gene discovery and further analysis of this species. The ''M. florum'' genome has been fully annotated. The method employed for sequencing the genome was Whole Genome Shotgun, where DNA is isolated from ''M. florum'' and cut into smaller fragments. These DNA fragments are then inserted into and vector and cloned, and both ends of the DNA fragments are sequenced, which produces paired reads. The paired reads are used to identify contigs, (contiguous stretches of sequence) which are ordered into supercontigs. (1) | ||
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==Cell structure and metabolism== | ==Cell structure and metabolism== | ||
Because of their small genome structure, ''M. florum'' have limited metabolic and biosynthetic capacity. This is because of its evolution from cell-walled gram-positive Firmicutes, which have a low G+C content. As the Mollicutes evolved, (including ''M. florum'') they increasingly become smaller in size, thus they evolved toward a small genome size, thus making itself dependent on the nutrients that its environment provides. This evolution toward small size is the reason why Mollicutes, as well as ''M. florum,'' have lost many of the genes that are involved in biosynthesis of lipids, amino acids, cofactors, and and gram-positive type cell wall components, as well as genes involved in transcription regulation, heat shock response, and cell division. Furthermore, they are deficient intermediate energy metabolism, and therefore depend on glycolysis as a source of ATP. The ATP can be synthesized via the glycolytic pathway or lactic fermentation. The above mentioned deficiencies are why ''M. florum'' depend so heavily on its surroundings as a source of nutrients. The reduction in size of the genome was heavily due to the above mentioned loss of metabolic pathways. (6) | Because of their small genome structure, ''M. florum'' have limited metabolic and biosynthetic capacity. This is because of its evolution from cell-walled gram-positive ''Firmicutes'', which have a low G+C content. As the ''Mollicutes evolved'', (including ''M. florum'') they increasingly become smaller in size, thus they evolved toward a small genome size, thus making itself dependent on the nutrients that its environment provides. This evolution toward small size is the reason why ''Mollicutes'', as well as ''M. florum,'' have lost many of the genes that are involved in biosynthesis of lipids, amino acids, cofactors, and and gram-positive type cell wall components, as well as genes involved in transcription regulation, heat shock response, and cell division. Furthermore, they are deficient intermediate energy metabolism, and therefore depend on glycolysis as a source of ATP. The ATP can be synthesized via the glycolytic pathway or lactic fermentation. The above mentioned deficiencies are why ''M. florum'' depend so heavily on its surroundings as a source of nutrients. The reduction in size of the genome was heavily due to the above mentioned loss of metabolic pathways. (6) | ||
For Mollicutes, cholesterol is a requirement for growth. (6) Sugars are used as a source of carbon and for energy for glycolysis. Furthermore, the pentose phosphate pathway is incomplete in Mollicutes. However, genes the encode enzymes of the tricarboxylic acid cycle are absent from the genomes. (7) Although ''M. florum'' have evolved to such a small size, they can rapidly adapt to their surroundings and to environmental changes. They also exhibit a high mutation rate and do not have an SOS response. (1) | For ''Mollicutes'', cholesterol is a requirement for growth. (6) Sugars are used as a source of carbon and for energy for glycolysis. Furthermore, the pentose phosphate pathway is incomplete in ''Mollicutes''. However, genes the encode enzymes of the tricarboxylic acid cycle are absent from the genomes. (7) Although ''M. florum'' have evolved to such a small size, they can rapidly adapt to their surroundings and to environmental changes. They also exhibit a high mutation rate and do not have an SOS response. (1) | ||
==Ecology== | ==Ecology== | ||
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The entire genome sequence has been sequenced. Further research being conducted on ''M. florum'' by Dr. Knight has led to the discovery that ''Mesoplasma florum'' and ''Mesoplasma entomophilum'' are likely to be the same species, as implied by their 100% identical 16S ribosomal DNA regions. Furthermore, research has led to yet another discovery, that ''M. florum'' is antibiotic resistant. Current research being conducted is characterization of ''M. florum'' proteins through gel electrophoresis and mass spectroscopy, which will lead to identification of coding sequences of genes. Enzymatic pathways will be discovered through metabolic modeling of ''M. florum'' and a biological system will be created. (9) | The entire genome sequence has been sequenced. Further research being conducted on ''M. florum'' by Dr. Knight has led to the discovery that ''Mesoplasma florum'' and ''Mesoplasma entomophilum'' are likely to be the same species, as implied by their 100% identical 16S ribosomal DNA regions. Furthermore, research has led to yet another discovery, that ''M. florum'' is antibiotic resistant. Current research being conducted is characterization of ''M. florum'' proteins through gel electrophoresis and mass spectroscopy, which will lead to identification of coding sequences of genes. Enzymatic pathways will be discovered through metabolic modeling of ''M. florum'' and a biological system will be created. (9) | ||
Research is being conducted into the nonsense codon UGA codes, as this change is believed to be related to the low G+C % of Mycoplasma. Furthermore, many metabolic functions are no longer needed (as displayed by the small genome size) and this also a current topic being researched. This large loss of genes can be noted by the genome sequence. Also, the loss of the cell wall is believed to be a result of intracellular endoparasitism. Comparative genomics is important in terms of ''M. florum'' because there is a large number of mycoplasma species with sequenced genomes, most of which are pathogenic. Because ''M. florum'' is non-pathogenic, it can be used when studying host-specific chronic diseases in humans and animals and when | Research is being conducted into the nonsense codon UGA codes, as this change is believed to be related to the low G+C % of Mycoplasma. Furthermore, many metabolic functions are no longer needed (as displayed by the small genome size) and this also a current topic being researched. This large loss of genes can be noted by the genome sequence. Also, the loss of the cell wall is believed to be a result of intracellular endoparasitism. Comparative genomics is important in terms of ''M. florum'' because there is a large number of mycoplasma species with sequenced genomes, most of which are pathogenic. Because ''M. florum'' is non-pathogenic, it can be used when studying host-specific chronic diseases in humans and animals and when creating antibiotics. (10) | ||
==References== | ==References== | ||
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(10) “Agent of the Murine Respiratory Mycoplasmosis.” Mycoplasma pulmonis UAB CTIP, Accessed August 22, 2007, <http://www.cns.fr/externe/English/Projets/Projet_AQ/organisme_AQ.html> | (10) “Agent of the Murine Respiratory Mycoplasmosis.” Mycoplasma pulmonis UAB CTIP, Accessed August 22, 2007, <http://www.cns.fr/externe/English/Projets/Projet_AQ/organisme_AQ.html> | ||
Edited by Lori Guner, student of Rachel Larsen | |||
KMG | |||
Latest revision as of 03:22, 20 August 2010
Classification
Higher order taxa
Bacteria; Firmicutes; Mollicutes; Entomoplasmatales; Entomoplasmataceae; Mesoplasma
Species
Mesoplasma florum
|
NCBI: Taxonomy |
Description and significance
Mesoplasma florum is a Mycoplasma species, which come from the bacteria Mollicutes. Mollicutes do not have a cell wall and are parasitic to humans, animals, and plants. Mycoplasma are characteristically small, as well as self-replicating. Although Mesoplasma florum are a species of Mycoplasma, Mesoplasma florum are not parasitic and are non-motile, unlike Mycoplasma. Like Mycoplasma, Mesoplasma florum are also have a very small genome size (smaller than 1Mb). (1) Mesoplasma florum was isolated from the flower of a lemon tree, and is therefore thought to be associated with plant insect vectors. (5)
Gene sequencing of Mesoplasma florum is important because it is the smallest self-replicating organism, Mycoplasma, and therefore, is itself very small. Furthermore, Mecoplasma florum is non-motile, so it is used to study and identify genes that are linked to motility.(1) Researchers working with Mesoplasma florum can use this species to understand why it has evolved to be non-motile even though Mycoplasma are motile, as well as why it has evolved to become non-parasitc. This shows us that Mycoplasma are highly evolving, and therefore are highly successful, therefore, gene sequencing of Mesoplasma florum is important because it is important in learning as to why Mesoplasma florum have evolved the way that it has. (2) As a result of their small genomes, they do not have a lot of metabolic ability. (2) They can easily adapt to their environment, even if that environment is changing. (1) This is important because Mesoplasma florum, as well as all species of Mycoplasma, uptake their nutrients from their environment. (3) Therefore, it is important to understand why this organism can thrive by uptaking nutrients which are continually changing.
Mesoplasma florum is not closely related to Mycoplasma genitalium and Mycoplasma pneumoniae. Although sterol is required in media for growth of Mollicutes, Mesoplasma florum does not require sterol. (1)
Genome structure
M. florum has a uniquely small genome size (smaller than 1Mb), due to its evolution from Mycoplasmas, which evolved from Gram-positive bacteria by reducing genome size many times. Mesoplasma florum has another unique genome characteristic in that in Mycoplasmas, the stop codon, UGA, has been changed to be translated as tryptophan. (1) (See Current research for further information).
Currently, genome sequencing for M. florum is being performed by Tom Knight, Senior Research Scientist at the MIT Artificial Intelligence Laboratory and the MIT Electrical Engineering and Computer Science Department, and the Broad Institute of MIT and Harvard. The Mesoplasma florum project will eventually yield gene discovery and further analysis of this species. The M. florum genome has been fully annotated. The method employed for sequencing the genome was Whole Genome Shotgun, where DNA is isolated from M. florum and cut into smaller fragments. These DNA fragments are then inserted into and vector and cloned, and both ends of the DNA fragments are sequenced, which produces paired reads. The paired reads are used to identify contigs, (contiguous stretches of sequence) which are ordered into supercontigs. (1)
M. florum has a circular genome that is 793,224 bp in size. It has a G+C content of 27.02%. (1) In M. florum, UGA encodes tryptophan in the rsp3 gene. (4) This bacterium has only 682 genes.
Cell structure and metabolism
Because of their small genome structure, M. florum have limited metabolic and biosynthetic capacity. This is because of its evolution from cell-walled gram-positive Firmicutes, which have a low G+C content. As the Mollicutes evolved, (including M. florum) they increasingly become smaller in size, thus they evolved toward a small genome size, thus making itself dependent on the nutrients that its environment provides. This evolution toward small size is the reason why Mollicutes, as well as M. florum, have lost many of the genes that are involved in biosynthesis of lipids, amino acids, cofactors, and and gram-positive type cell wall components, as well as genes involved in transcription regulation, heat shock response, and cell division. Furthermore, they are deficient intermediate energy metabolism, and therefore depend on glycolysis as a source of ATP. The ATP can be synthesized via the glycolytic pathway or lactic fermentation. The above mentioned deficiencies are why M. florum depend so heavily on its surroundings as a source of nutrients. The reduction in size of the genome was heavily due to the above mentioned loss of metabolic pathways. (6)
For Mollicutes, cholesterol is a requirement for growth. (6) Sugars are used as a source of carbon and for energy for glycolysis. Furthermore, the pentose phosphate pathway is incomplete in Mollicutes. However, genes the encode enzymes of the tricarboxylic acid cycle are absent from the genomes. (7) Although M. florum have evolved to such a small size, they can rapidly adapt to their surroundings and to environmental changes. They also exhibit a high mutation rate and do not have an SOS response. (1)
Ecology
Mesoplasma florum was originally recovered from the flower of a lemon tree. (5) M. florum is associated with plant insect vectors. However, its primary vector has not yet been identified. (1) There is not much research that has been done to provide information on M. florum's interaction with other organisms. Because M. florum is non-pathogenic, information about its effects on humans, plants, or animals is not available. However, M. florum is known to be highly dependent on its surroundings, and therefore its survival is also dependent on the nutrients provided by its surroundings. Therefore, an environment with cholesterol and sugars is favored.
Pathology
Mesoplasma florum is non-pathogenic, and therefore there are no known diseases that are related to this organism.
Application to Biotechnology
Mesoplasma florum may be used in future engineering of reduced complexity living cells. Research that is currently being conducted on M. florum at the Broad Institute of MIT and Harvard, by Dr. Knight will be useful in studying and treating various diseases. Because they are good representatives of organisms with small genome size and small cell size, they are unique. The research being conducted on M. florum will be used as a model for genetic analysis of pathogens, as well as for genetic analysis of minimal genomes. Because M. florum is not motile, research being conducted on it may also be used in the identification of motility genes. (1)
With the discovery of the genome sequence, many of the pathways that were lost during evolution may be reconstructed and used to to understand why M. florum evolved to such a state. With genome sequencing, many of the sequences in the M. florum which were lost have been identified through Shotgun Sequencing. Through research with M. florum, this organism may be used to build a minimal organism, which can be engineered by removing genes. This type of research can be used to produce vitamins, hormones, enzymes, or cytokines for humans. (8) In essence, Dr. Knight and his team are engineering a biological system.
Current Research
Because M. florum can be conveniently grown and has a minimal genome sequence, it is ideal for research on small organisms. (8) Its DNA segments are being used by the Broad Institute of MIT and Harvard to build and test functional biological systems and to build a minimal organism. (8) These biological systems can be taken into use for medicinal applications, as well as in agriculture. Non essential genes can be removed for analysis, and a minimal organism with only the essential genes may be built.
The entire genome sequence has been sequenced. Further research being conducted on M. florum by Dr. Knight has led to the discovery that Mesoplasma florum and Mesoplasma entomophilum are likely to be the same species, as implied by their 100% identical 16S ribosomal DNA regions. Furthermore, research has led to yet another discovery, that M. florum is antibiotic resistant. Current research being conducted is characterization of M. florum proteins through gel electrophoresis and mass spectroscopy, which will lead to identification of coding sequences of genes. Enzymatic pathways will be discovered through metabolic modeling of M. florum and a biological system will be created. (9)
Research is being conducted into the nonsense codon UGA codes, as this change is believed to be related to the low G+C % of Mycoplasma. Furthermore, many metabolic functions are no longer needed (as displayed by the small genome size) and this also a current topic being researched. This large loss of genes can be noted by the genome sequence. Also, the loss of the cell wall is believed to be a result of intracellular endoparasitism. Comparative genomics is important in terms of M. florum because there is a large number of mycoplasma species with sequenced genomes, most of which are pathogenic. Because M. florum is non-pathogenic, it can be used when studying host-specific chronic diseases in humans and animals and when creating antibiotics. (10)
References
(1) Broad Institute: "Mesoplasma florum Sequencing Project at the Broad Institute," Accessed August 19, 2007, <http://www.broad.mit.edu/annotation/microbes/mesoplasma_florum/background.html#what>
(2) Hegemann, Johannes H., Henrich, Birgit, and Hopfe, Miriam. "HinT Proteins and their Putative Interaction Partners in Mollicutes and Chlamydiaceae," BMC Microbiol. 2005. 2005 May 18
(3) Ainsworth, Claire. "The Facts of Life." New Scientist Magazine. 2003 May 31.
(4) Department of Botany and Plant Pathology, Michigan State University, East Lansing 48824-1312, “Phylogenetic relationships among members of the class Mollicutes deduced from rps3 gene sequences,” Accessed August 20, 2007. <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8123554&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>
(5)HAMAP: Mesoplasma florum (Acholeplasma florum) complete proteome, Accessed August 20, 2007. <http://www.expasy.ch/sprot/hamap/MESFL.html>
(6) Arraes, Fabricio B.M, Brigido, Marcelo M., Felipe, Maria Sueli S., Carvalho, Jose A. de, Maranhao, Andrea Q, and Pedrosa, Fabio O. “Differential metabolism of Mycoplasma species as revealed by their genomes.” 2006 October 9
(7) Halbedel, Sven, Hames, Claudine, and Stülke, Jörg. “Regulation of carbon metabolism in the mollicutes and its relation to virulence,” Journal of Molecular Microbiology and Biotechnology, 2007; 12: 147-154.
(8) Freitas, Robert A. Jr. and Merkle, Ralph C. “Artificial Biological Replicators,” Kinematic Self-Replicating Machines, 2004.
(9) Knight, Thomas F. Jr. “Digital control and communication in living cells,” Accessed August 21, 2007, <http://www.ai.mit.edu/projects/ntt/documents/biannual0012/MIT9904-10/report.pdf>
(10) “Agent of the Murine Respiratory Mycoplasmosis.” Mycoplasma pulmonis UAB CTIP, Accessed August 22, 2007, <http://www.cns.fr/externe/English/Projets/Projet_AQ/organisme_AQ.html>
Edited by Lori Guner, student of Rachel Larsen
KMG
