Difference between revisions of "Sinorhizobium meliloti"

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Sinorhizobium
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''Sinorhizobium''
meliloti;
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''meliloti'';
  
 
==Description and significance==
 
==Description and significance==
  
Sinorhizobium meliloti is a gram-negative bacterium.  As are other Rhizobia, S. meliloti can be found as a normal, free-living microorganisms in the soil (10).  However, it is for their nitrogen-fixing symbiotic relationships with legumes that S. meliloti are studied.  S. meliloti cells detect substances particularly made up of amino and organic acids, released by the roots of plants.  The cells are drawn toward root hairs that emerge from the roots and induce the root hair tips to curl up.  There is a cytoplasmic bridge formed by the microtubules and the cytoplasm of the root cells.  This bridge guides infection threads extending from the roots to the cortex of the bacterial cells.  Finally, the S. meliloti cells enter the cytoplasm of the root cells through endocytosis.  S. meliloti transform atmospheric nitrogen into a form that may be utilized by the host in which they reside.  Also, the S. meliloti is significant in that it leaves behind excess nitrogen in the soil which may potentially reduce the need for fertilizers (5).  The S. meliloti genome was isolated and sequenced from nodules and soil primarily from host plants such as the Medicago (alfalfa and perennial and annual medics), Melilotus (sweet clover), and Trigonella (fenugreek) species (10). The detailed study of S. meliloti and other Rhizobia will further inform microbiologists about how these bacteria colonize root surfaces of their host and what mechanisms make-up the complex rhizobium-legume symbiotic relationship (2).
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''Sinorhizobium'' ''meliloti'' is a gram-negative bacterium.  As are other Rhizobia, ''S.'' ''meliloti'' can be found as normal, free-living microorganisms in the soil (11).  However, it is for its nitrogen-fixing symbiotic relationships with legumes that ''S.'' ''meliloti'' is studied.  ''S.'' ''meliloti'' cells detect substances particularly made up of amino and organic acids, released by the roots of plants (12).  The cells are drawn toward root hairs that emerge from the roots and induce the root hair tips to curl up.  There is a cytoplasmic bridge formed by the microtubules and the cytoplasm of the root cells.  This bridge guides infection threads extending from the roots to the cortex of the bacterial cells.  Finally, the ''S.'' ''meliloti'' cells enter the cytoplasm of the root cells through endocytosis (1)''S.'' ''meliloti'' transform atmospheric nitrogen into a form that may be utilized by the host in which they reside (12).  Also, the ''S.'' ''meliloti'' is significant in that it leaves behind excess nitrogen in the soil which may potentially reduce the need for fertilizers (7).  The ''S.'' ''meliloti'' genome was isolated and sequenced from nodules and soil primarily from host plants such as the Medicago (alfalfa and perennial and annual medics), Melilotus (sweet clover), and Trigonella (fenugreek) species (11). The detailed study of ''S.'' ''meliloti'' and other Rhizobia will further inform microbiologists about how these bacteria colonize root surfaces of their host and what mechanisms make-up the complex rhizobium-legume symbiotic relationship (12).
  
 
==Genome structure==
 
==Genome structure==
  
S. meliloti is a fast growing Rhizobium that has a moderately small genome size of 6.7 Million base pairs.  The genome is still quite complex and is made up of three circular elements of DNA, also known as replicons.  One is a single chromosome 3.65 Mb long, while the other two are megaplasmids 1.68 Mb and 1.35 Mb long a piece.  Each replicon contributes to a certain degree to the bacteria's symbiosis with the plant.  The largest replicon is responsible for all the housekeeping genes of S. meliloti cells, in particular the genes responsible for metabolic pathways.  Also, it carries the genes involved in plant interaction, responding to external stress, mobility, and chemotaxis.  The second replicon, named pSymB, carries genes involved in nutrient uptake and effective invasion of the plant host.  The third and smallest replicon, named pSymA, is responsible for the the nitrogen-fixing capabilities of the bacterium.  All three chromosomal components have been sequenced by researchers from around the world.
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''S.'' ''meliloti'' is a fast growing Rhizobium that has a moderately small genome size of 6.7 Million base pairs.  The genome is still quite complex and is made up of three circular elements of DNA, also known as replicons (5).  One is a single chromosome 3.65 Mb long, while the other two are megaplasmids 1.68 Mb and 1.35 Mb long a piece (7).  Each replicon contributes to the bacteria's symbiosis with its host plant.  The largest replicon is responsible for all the housekeeping genes of ''S.'' ''meliloti'' cells, in particular the genes responsible for metabolic pathways.  Also, it carries the genes involved in plant interaction, responding to external stress, mobility, and chemotaxis.  The second replicon, named pSymB, carries genes involved in nutrient uptake and effective invasion of the plant host.  The third and smallest replicon, named pSymA, is responsible for the the nitrogen-fixing capabilities of the bacterium (5).  All three chromosomal components have been sequenced by researchers from around the world.
  
 
==Cell structure and metabolism==
 
==Cell structure and metabolism==
  
S. meliloti is an aerobic bacterium that can be found either living independently in soil or on the roots of leguminous plants.  A single superoxide dismutase, coded for by the sodA gene,  catalyses the formation of hydrogen peroxide and oxygen from superoxides.  S. meliloti cells will encounter two strikingly different environments during their life time, the soil and the nodules formed on the roots of plants.  In the soil there is a large abundance of manganese that the cell can use and undergo aerobiosis.  However, in the nodules there is a very low concentration of free oxygen and manganese where as iron is abundant in this highly acidic environment.  In such conditions, it is favorable for the S. meliloti cells to utilize an iron-substituted superoxide dismutatse.  It is most probably because the S. meliloti cells transition from the aerobic cycle in the soil to the microaerobic cycle in the nodule environment that they developed a cambialistic superoxide dismutase.   
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''S.'' ''meliloti'' is an aerobic bacterium that can be found either living independently in soil or on the roots of leguminous plants (14).  A single superoxide dismutase, coded for by the sodA gene,  catalyses the formation of hydrogen peroxide and oxygen from superoxides (14)''S.'' ''meliloti'' cells will encounter two strikingly different environments during their life time, the soil and the nodules formed on the roots of plants (4).  In the soil there is a large abundance of manganese that the cell can use and undergo aerobiosis.  However, in the nodules there is a very low concentration of free oxygen and manganese where as iron is abundant in this highly acidic environment (9).  In such conditions, it is favorable for the ''S.'' ''meliloti'' cells to utilize an iron-substituted superoxide dismutatse (15).  It is most probably because the ''S.'' ''meliloti'' cells transition from the aerobic cycle in the soil to the microaerobic cycle in the nodule environment that they developed a cambialistic superoxide dismutase (14).   
  
  
S. meliloti and root cells of legumes share a symbiotic relationship in which the bacterial cells fix atmospheric nitrogen into a usable form by the root cells.  In return the plant cells produce reduced carbon compounds that the S. meliloti can uptake as their carbon source.  Among the several possible carbon sources available to the S. meliloti cells, dicarboxylic acids such as succinate, fumerate, and malate are preferred because of their involvment in nitrogen fixation.  The oxidation of these compounds is essential for S. melioti cells to be able to fix atmospheric nitrogen into a usable form for leguminous plants.  Using these compounds allows the bacterial cells to maintain a fast growth rate as well. The uptake of succinate in preference to other carbon sources is known as succinate-mediated catabolite repression and it varies from the catabolite repression in other bacteria.  The exact molecular mechanisms of the succinate-mediated catabolite repression is yet to be cleared up.  One key note to make about S. meliloti is that their carbon sources do not enter the Phosphate Transfer System because the cells have an incomplete PTS and thus enter through a transporter known as the DctA permease.  The bacterial cells synthesizes several polysaccharides including glycogen, cyclic Beta-glucans, and exopolysaccharides.  The biosynthetic pathways utilized by the cells include the Entner-Doudoroff and pentose-phosphate pathways with glucose 6-phosphate serving key enzymatic purposes.
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''S.'' ''meliloti'' and root cells of legumes share a symbiotic relationship in which the bacterial cells fix atmospheric nitrogen into a usable form by the root cells (12).  In return the plant cells produce reduced carbon compounds that the ''S.'' ''meliloti'' can uptake as their carbon source.  Among the several possible carbon sources available to the ''S.'' ''meliloti'' cells, dicarboxylic acids such as succinate, fumerate, and malate are preferred because of their involvement in nitrogen fixation (13).  The oxidation of these compounds is essential for ''S.'' ''melioti'' cells to be able to fix atmospheric nitrogen into a usable form for leguminous plants.  Using these compounds allows the bacterial cells to maintain a fast growth rate as well. The uptake of succinate in preference to other carbon sources is known as succinate-mediated catabolite repression and it varies from the catabolite repression in other bacteria (10).  The exact molecular mechanisms of the succinate-mediated catabolite repression is yet to be cleared up.  One key note to make about ''S.'' ''meliloti'' is that their carbon sources do not enter the Phosphate Transfer System because the cells have an incomplete PTS and thus enter through a transporter known as the DctA permease (13).  The bacterial cells synthesize several polysaccharides including glycogen, cyclic Beta-glucans, and exopolysaccharides.  The biosynthetic pathways utilized by the cells include the Entner-Doudoroff and pentose-phosphate pathways with glucose 6-phosphate serving key enzymatic purposes (13).
  
 
==Ecology==
 
==Ecology==
  
As other soil bacteria, Sinorhizobium meliloti cells serve a significant role in the survival of many plant species, and they also make a large contribution to the environment as a whole. The atmosphere is made up of approximately 85% nitrogen and it is thus an essential element to most living organisms and their biological processes.  However, nitrogen is present in the atmosphere in the form of dinitrogen (N2) which is unusable by most plants and animals.  S. meliloti cells serve a very crucial role in the environment in that they form symbiotic relationships with leguminous plants and convert N2 into organic nitrogen.  This mutual relationship benefits the plants by providing them a readily available source of a very essential nutrient.   
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As other soil bacteria, ''Sinorhizobium'' ''meliloti'' cells serve a significant role in the survival of many plant species, and they also make a large contribution to the environment as a whole (12). The atmosphere is made up of approximately 85% nitrogen and it is thus an essential element to most living organisms and their biological processes.  However, nitrogen is present in the atmosphere in the form of dinitrogen (N2) which is unusable by most plants and animals (8)''S.'' ''meliloti'' cells serve a very crucial role in the environment in that they form symbiotic relationships with leguminous plants and convert N2 into organic nitrogen.  This mutual relationship benefits the plants by providing them a readily available source of a very essential nutrient.   
  
Interestingly, S. meliloti is also capable of denitrification as well.  Denitrification is the process of reducing nitrate and nitrite into N2 which is more abundant in the environment.  S. meliloti is unique in that it is one of the first organisms to have a cluster of all four nitrogen oxide reductases (nap, nir, nor, nos) on the same chromosome.  Denitrification can have hazardous effects such as a loss of biologically useful nitrogen, a build up of N2O as a byproduct which contributes to acidic rain, and a depletion of the ozone layer.  However, denitrification conducted by S. meliloti cells can have positive effects as well if it is harnessed in the correct way.  For example, the N2O produced by denitrification can serve as a green-house gas that traps heat.  Also, microbial denitrification can contribute significantly to the purification of wastewater.  Nitrogen-rich fertilizers have contributed to the pollution of ground water.  This water is potentially hazardous to pregnant women and infants and thus scientists are considering using microbial denitrification in water treatment facilities to remove excess NO3.
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Interestingly, ''S.'' ''meliloti'' is also capable of denitrification as well.  Denitrification is the process of reducing nitrate and nitrite into N2 which is more abundant in the environment.  ''S.'' ''meliloti'' is unique in that it is one of the first organisms to have a cluster of all four nitrogen oxide reductases (nap, nir, nor, nos) on the same chromosome (8).  Denitrification can have hazardous effects such as a loss of biologically useful nitrogen, a build up of N2O as a byproduct which contributes to acidic rain, and a depletion of the ozone layer.  However, denitrification conducted by ''S.'' ''meliloti'' cells can have positive effects as well if it is harnessed in the correct way.  For example, the N2O produced by denitrification can serve as a green-house gas that traps heat.  Also, microbial denitrification can contribute significantly to the purification of wastewater.  Nitrogen-rich fertilizers have contributed to the pollution of ground water (7).  This water is potentially hazardous to pregnant women and infants and thus scientists are considering using microbial denitrification in water treatment facilities to remove excess NO3 (8).
  
 
==Pathology==
 
==Pathology==
  
Since Sinorhizobium meliloti is a nitrogen fixing soil bacteria, its primary purpose is to undergo reactions to assist plants.  It does not have any pathogenic characteristics, rather it maintains a symbiotic relationship with leguminous plants and ultimately betters the environment.  S. meliloti cells, however, do conduct denitrification in addition to nitrogen fixation, and this process has known side effects to the environment.  As mentioned above, excess denitrification can deplete the environment of a usable nitrogen source, result in a build up of N2O which contributes to acidic rain, and deplete the ozone layer.  Whether or not S. meliloti cells directly contribute negatively to the environment as a result of their denitrification still remains under investigation.
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Since ''Sinorhizobium'' ''meliloti'' is a nitrogen fixing soil bacteria, its primary purpose is to undergo reactions to assist plants.  It does not have any pathogenic characteristics, rather it maintains a symbiotic relationship with leguminous plants and ultimately betters the environment (12)''S.'' ''meliloti'' cells, however, do conduct denitrification in addition to nitrogen fixation, and this process has known side effects to the environment.  As mentioned above, excess denitrification can deplete the environment of a usable nitrogen source, result in a build up of N2O which contributes to acidic rain, and deplete the ozone layer (8).  Whether or not ''S.'' ''meliloti'' cells directly contribute negatively to the environment as a result of their denitrification still remains under investigation.
  
 
==Application to Biotechnology==
 
==Application to Biotechnology==
  
S. meliloti cells are currently being used by microbiologists to further study plants and nutrient composition in the wild.  Using these bacterial cells as a technology to further research is an example of microbial ecology.  By learning the details that involve plant/microbe interactions, researchers can determine the correlation between the presence of certain compounds and the ability of plants to take them up.  However, studying nutrients near the root of plants can prove challenging.  The nutrients are often readily taken up by microorganisms that reside in the root region and thus it is difficult to isolate the root region without changing nutrient distributions.  The symbiotic relationship that S. meliloti and other Rhizobia share with legumes is being utilized by microbial ecologists to fix this issue.  Bacterial cells are stained with dies that flouresce only in the presence of certain nutrients in the root or the soil.  The biosensing bacteria are added to plants and they illuminate to indicate regions where particular nutrients are present.  Such technology has indicated nutrients, their distributions, their depletion and their uptake around plant roots and in the soil.  In particular, such biotechnology is used to study to which extent sugars, organic acids, and bulk carbon support the growth of bacteria in varying plant species.
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''S.'' ''meliloti'' cells are currently being used by microbiologists to further study plants and nutrient composition in the wild.  Using these bacterial cells as a technology to further research is an example of microbial ecology.  By learning the details that involve plant/microbe interactions, researchers can determine the correlation between the presence of certain compounds and the ability of plants to take them up (4).  However, studying nutrients near the root of plants can prove challenging.  The nutrients are often readily taken up by microorganisms that reside in the root region and thus it is difficult to isolate the root region without changing nutrient distributions.  The symbiotic relationship that ''S.'' ''meliloti'' and other Rhizobia share with legumes is being utilized by microbial ecologists to fix this issue (3).  Bacterial cells are stained with dies that flouresce only in the presence of certain nutrients in the root or the soil.  The biosensing bacteria are added to plants and they illuminate to indicate regions where particular nutrients are present(3).  Such technology has indicated nutrients, their distributions, their depletion and their uptake around plant roots and in the soil.  In particular, such biotechnology is used to study to what extent sugars, organic acids, and bulk carbon support the growth of bacteria in varying plant species.
  
In addition, currently a study is underway to investigate the usefulness of Sinorhizobium meliloti in purifying drinking water because of the denitrification that it undergoes to convert NO3 to N2 and N2O.  If proven effective, S. meliloti cells would be used in water treatment facilities in addition to other filters.
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In addition, currently a study is underway to investigate the usefulness of ''Sinorhizobium'' ''meliloti'' in purifying drinking water because of the denitrification that it undergoes to convert NO3 to N2 and N2O.  If proven effective, ''S.'' ''meliloti'' cells would be used in water treatment facilities in addition to other filters (8).
  
 
==Current Research==
 
==Current Research==
  
1) The Australian National University - Research School of Biological Sciences is currently evaluating the methods by which undifferentiated cells of plants undergo development and how plants respond to bacterial infection.  This team of researchers is aiming to approach plant biology with both molecular biology as well as genetics.  Sinorhizobium meliloti cells have a model relationship with the legume roots that they often reside on. The team is using this model interaction as the basis of their study in order to determine which specific genes, gene products, and signaling molecules regulate growth and development of the nodule meristem.  By isolating novel peptide signal molecules that may act as regulators or proliferating meristemic cells, they may be able to manipulate plants for adaption to the Australian environment and even for the production of chemicals that are beneficial to human cells.  Finally, the research team is investigating the genome of the microsymbiont S. meliloti cells in order to determine an overall metabolic framework for these cells.  This bacteria can adjust to several lifestyles, either to that of the nutrient-poor soil, the plant rhizosphere, and the inside of root nodules.  They aim to determine which proteins allow them to thrive under various conditions.   
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1) The Australian National University - Research School of Biological Sciences is currently evaluating the methods by which undifferentiated cells of plants undergo development and how plants respond to bacterial infection.  This team of researchers claims  to approach plant biology with both molecular biology as well as genetics.  ''Sinorhizobium'' ''meliloti'' cells have a model relationship with the legume roots that they often reside on. The team is using this model interaction as the basis of their study in order to determine which specific genes, gene products, and signaling molecules regulate growth and development of the nodule meristem.  By isolating novel peptide signal molecules that may act as regulators for proliferating meristemic cells, they may be able to manipulate plants for adaption to the Australian environment and even for the production of chemicals that are beneficial to human cells.  Finally, the research team is investigating the genome of the microsymbiont ''S.'' ''meliloti'' cells in order to determine an overall metabolic framework for these cells.  This bacteria can adjust to several lifestyles, either to that of the nutrient-poor soil, the plant rhizosphere, and the inside of root nodules.  They aim to determine which proteins allow them to thrive under various conditions (14).   
  
2) Recently, The National Laboratory of Plant Molecular Genetics, as well as other notable institutes in China, have investigated the specific genes of S. meliloti that contribute to its nitrogen fixation abilities.  The Rhizobium nifA gene is an activator of nitrogen fixation and it causes its effects in nodule bacteria.  To further understand the effects of the Sinorhizobium meliloti nifA gene on Alfalfa plants, the cDNA-AFLP technique was implemented to monitor the changes in gene expression in nifA mutant nodules.  The purpose of this investigation was to determine whether or not the S. meliloti nifA mutant causes a different gene expression profile from the wild type gene in Alfalfa nodules.   
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2) Recently, The National Laboratory of Plant Molecular Genetics, as well as other notable institutes in China, have investigated the specific genes of ''S.'' ''meliloti'' that contribute to its nitrogen fixation abilities.  The Rhizobium nifA gene has been determined to be an activator of nitrogen fixation as it causes its effects in nodule bacteria.  To further understand the effects of the ''Sinorhizobium'' ''meliloti'' nifA gene on Alfalfa plants, the cDNA-AFLP technique was implemented to monitor the changes in gene expression in nifA mutant nodules.  The purpose of this investigation was to determine whether or not the ''S.'' ''meliloti'' nifA mutant causes a different gene expression profile from the wild type gene in Alfalfa nodules (6).   
  
3) Dublin University is currently examining the mechanisms of siderophore mediated iron acquisition by Sinorhizobium meliloti.  In the root nodules of  plants, there is a high abundance of iron and a very low pH.  S. meliloti cells, as mentioned above, utilize and iron-substituted superoxide dismutase to obtain their source of oxygen.  Sidereophores dissolve ions of Fe3+ and allow cells to take it up via active transport mechanisms.  Researchers are interested in identifying and characterizing the membrane proteins that function in siderophore recognition and transport.
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3) Dublin University is currently examining the mechanisms of siderophore-mediated iron acquisition by ''Sinorhizobium'' ''meliloti''.  In the root nodules of  plants, there is a high abundance of iron and a very low pH.  ''S.'' ''meliloti'' cells, as mentioned above, utilize an iron-substituted superoxide dismutase to obtain their source of oxygen.  Sidereophores dissolve ions of Fe3+ and allow cells to take them up via active transport mechanisms.  Researchers are interested in identifying and characterizing the membrane proteins that function in siderophore recognition and transport (9).
  
 
==References==
 
==References==
  
1. A Lambert, M Osteras, K Mandon, M C Poggi, D Le Rudulier, "Fructose uptake in Sinorhizobium meliloti is mediated by a high-affinity ATP-binding cassette transport system", International Bibliographic Information on Dietary Supplements, 183(16): 4709-17, Auguest 2001, http://grande.nal.usda.gov/ibids/index.php?mode2=detail&origin=ibids_references&therow=447491
 
  
2. Anne Milcamps, Paolo Struffi, and Frans J. de Bruijn, "The Sinorhizobium meliloti Nutrient-Deprivation-Induced Tyrosine Degradation Gene hmgA Is Controlled by a Novel Member of the arsR Family of Regulatory Genes", Applied and Environmental Microbiology, 67(6): 2641–2648, doi: 10.1128/AEM.67.6.2641-2648.2001, June 2001,  
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1. Ampe, F., Kiss, E., Sabourdy, F., and Batut, J., “Transcriptome analysis of ''Sinorhizobium'' ''meliloti'' during symbiosis”, Genome Biology, 4:R15    doi:10.1186/gb-2003-4-2-r15, 2003,  
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=92919
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http://genomebiology.com/2003/4/2/R15
  
3. Barnett MJ et al., "A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.", Proc Natl Acad Sci U S A, 2004 Nov 23;101(47):16636-41
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2. Barnett, MJ et al., "A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.", Proc Natl Acad Sci U S A, 2004 Nov 23;101(47):16636-41 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=19  
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=19
 
  
4. Barry Rolfe, "Genomic Interactions", Australian Research Council Centre of Excellence for Integrative Legume Research, 12 March 2007,
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3. Bringhurst, R. M., Cardon, Z., and Gage D. J., "Galactosides in the rhizosphere: utilization by ''Sinorhizobium'' ''meliloti'' and development of a biosensor". Proc. Nat. Acad. Sci. 98:4540-4545, 2001 http://web.uconn.edu/gage/Notes/Publications/2001-biosensor%20PNAS%2098-4540.pdf
http://www.rsbs.anu.edu.au/ResearchGroups/GIG/index.php
 
  
5. Birgit Hofmann-Reinert, "In symbiosis with alfalfa: The complex genome sequence of Sinorhizobium meliloti", Genome News Network, August 6, 2001,
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4. Djordjevic, M. A., "''Sinorhizobium'' ''meliloti'' metabolism in the root nodule: a proteomic perspective", Australian Research Council Centre of Excellence for Integrative Legume Research, (Vol. 4) (No. 7) 1859-1872, 2004 http://www.cababstractsplus.org/google/abstract.asp?AcNo=20043149371
http://www.genomenewsnetwork.org/articles/08_01/Symbiosis.shtml
 
  
6. Bringhurst, R. M., Cardon, Z., and D. J. Gage, "Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor". Proc. Nat. Acad. Sci. 98:4540-4545, 2001
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5. Finan, T., Weidner, S., Wong, K., Buhrmester, J., Chain, P., Vorhölter, F., Hernandez-Lucas, I., Becker, A., Cowie, A., Gouzy, J., Golding, B., and Pühler, A., "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont ''Sinorhizobium'' ''meliloti''" Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 17, 9889-9894, August 14, 2001 http://bioinfo.genopole-toulouse.prd.fr/annotation/iANT/bacteria/rhime/  
http://web.uconn.edu/gage/Notes/Publications/2001-biosensor%20PNAS%2098-4540.pdf
 
  
7. Damien Keogh, Peter Collins, Paraic O Cuiv, "Iron Transport in Bacteria", Dublin City University, 2006, http://webpages.dcu.ie/~oconnelm/projects.html
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6. Gong, Z., He, ZS., Zhu, JB., Yu, GQ., and Zou, HS., "''Sinorhizobium'' ''meliloti'' nifA mutant induces different gene expression profile from wild type in Alfalfa nodules", 16: 818–829. doi: 10.1038/sj.cr.7310096, Sep 26 2006 http://www.nature.com/cr/journal/v16/n10/abs/7310096a.html  
  
8. Djordjevic, M. A., "Sinorhizobium meliloti metabolism in the root nodule: a proteomic perspective", Australian Research Council Centre of Excellence for Integrative Legume Research, (Vol. 4) (No. 7) 1859-1872, 2004
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7. Hofmann-Reinert, B., "In symbiosis with alfalfa: The complex genome sequence of ''Sinorhizobium'' ''meliloti''", Genome News Network, August 6, 2001, http://www.genomenewsnetwork.org/articles/08_01/Symbiosis.shtml
http://www.cababstractsplus.org/google/abstract.asp?AcNo=20043149371
 
  
9. Jean-Charles Portais, Patricia Tavernier, Isabelle Gosselin, Jean-Noël Barbotin, "Cyclic organization of the carbohydrate metabolism in Sinorhizobium meliloti", European Journal of Biochemistry, 265 (1), 473–480. doi:10.1046/j.1432-1327.1999.00778.x, October 1999, http://www.blackwell-synergy.com/doi/full/10.1046/j.1432-1327.1999.00778.x?prevSearch=allfield%3A%28Sinorhizobium+meliloti%29&cookieSet=1
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8. House, B., “Novel Methods of Manipulating The ''Sinorhizobium'' ''Meliloti'' Genome and Studying the Effects of Denitrification on symbiotic Nitrogen Fixation”, Washington State University, School of Molecular Biology, pg. 101-125, 2003,  
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https://research.wsulibs.wsu.edu:8443/dspace/bitstream/2376/98/1/b_house_050103.pdf
  
10. Marina L. Roumiantseva, Evgeny E. Andronov, Larissa A. Sharypova, Tatjana Dammann-Kalinowski, Mathias Keller, J. Peter W. Young, and Boris V. Simarov, "Diversity of Sinorhizobium meliloti from the Central Asian Alfalfa Gene Center", Applied and Environmental Microbiology, 68(9): 4694–4697. doi: 10.1128/AEM.68.9.4694-4697.2002, September 2002, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=124126
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9. Keogh D., Collins P., Cuiv P., "Iron Transport in Bacteria", Dublin City University, 2006, http://webpages.dcu.ie/~oconnelm/projects.html
  
11. Renata Santos, Stephane Bocquet, Alain Puppo, and Danièle Touati, "Characterization of an Atypical Superoxide Dismutase from Sinorhizobium meliloti", Journal of Bacteriology, 181(15): 4509–4516, 1999 August,
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10. Lambert, A., Osteras, M., Mandon, K., Poggi, M C., Le Rudulier, D., "Fructose uptake in ''Sinorhizobium'' ''meliloti'' is mediated by a high-affinity ATP-binding cassette transport system", International Bibliographic Information on Dietary Supplements, 183(16): 4709-17, Auguest 2001, http://grande.nal.usda.gov/ibids/index.php?mode2=detail&origin=ibids_references&therow=447491
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=103580
 
  
12. Turlough M. Finan, Stefan Weidner, Kim Wong, Jens Buhrmester, Patrick Chain, Frank J. Vorhölter, Ismael Hernandez-Lucas, Anke Becker, Alison Cowie, Jérôme Gouzy, Brian Golding, and Alfred Pühler, "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti"
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11. Marina L. Roumiantseva, Evgeny E. Andronov, Larissa A. Sharypova, Tatjana Dammann-Kalinowski, Mathias Keller, J. Peter W. Young, and Boris V. Simarov, "Diversity of ''Sinorhizobium'' ''meliloti'' from the Central Asian Alfalfa Gene Center", Applied and Environmental Microbiology, 68(9): 4694–4697. doi: 10.1128/AEM.68.9.4694-4697.2002, September 2002, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=124126
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 17, 9889-9894, August 14, 2001
 
http://bioinfo.genopole-toulouse.prd.fr/annotation/iANT/bacteria/rhime/
 
  
13. Zi Ying Gong, Zhi Shui He, Jia Bi Zhu, Guan Qiao Yu and Hua Song Zou, "Sinorhizobium meliloti nifA mutant induces different gene expression profile from wild type in Alfalfa nodules", 16: 818–829. doi: 10.1038/sj.cr.7310096, Sep 26 2006
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12. Milcamps, A., Struffi, P., and de Bruijn, F., "The ''Sinorhizobium'' ''meliloti'' Nutrient-Deprivation-Induced Tyrosine Degradation Gene hmgA Is Controlled by a Novel Member of the arsR Family of Regulatory Genes", Applied and Environmental Microbiology, 67(6): 2641–2648, doi: 10.1128/AEM.67.6.2641-2648.2001, June 2001, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=92919
http://www.nature.com/cr/journal/v16/n10/abs/7310096a.html
 
  
 +
13. Portais, J., Tavernier, P., Gosselin, I., Barbotin, J., "Cyclic organization of the carbohydrate metabolism in ''Sinorhizobium'' ''meliloti''", European Journal of Biochemistry, 265 (1), 473–480. doi:10.1046/j.1432-1327.1999.00778.x, October 1999, http://www.blackwell-synergy.com/doi/full/10.1046/j.1432-1327.1999.00778.x?prevSearch=allfield%3A%28Sinorhizobium+meliloti%29&cookieSet=1
  
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14. Rolfe, B., "Genomic Interactions", Australian Research Council Centre of Excellence for Integrative Legume Research, 12 March 2007, http://www.rsbs.anu.edu.au/ResearchGroups/GIG/index.php
 +
 +
15. Santos, R., Bocquet, S., Puppo, A., and Touati, D., "Characterization of an Atypical Superoxide Dismutase from ''Sinorhizobium'' ''meliloti''", Journal of Bacteriology, 181(15): 4509–4516, 1999 August, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=103580
  
  
 
Edited by Muna Beg, a student of [mailto:ralarsen@ucsd.edu Rachel Larsen]
 
Edited by Muna Beg, a student of [mailto:ralarsen@ucsd.edu Rachel Larsen]
 +
 +
Edited by KLB

Latest revision as of 15:53, 16 September 2010

This student page has not been curated.

A Microbial Biorealm page on the genus Sinorhizobium meliloti

Classification

Higher order taxa

Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiazeae; Sinorhizobium (2).


[Others may be used. Use NCBI link to find]

Species

NCBI: Taxonomy

Sinorhizobium meliloti;

Description and significance

Sinorhizobium meliloti is a gram-negative bacterium. As are other Rhizobia, S. meliloti can be found as normal, free-living microorganisms in the soil (11). However, it is for its nitrogen-fixing symbiotic relationships with legumes that S. meliloti is studied. S. meliloti cells detect substances particularly made up of amino and organic acids, released by the roots of plants (12). The cells are drawn toward root hairs that emerge from the roots and induce the root hair tips to curl up. There is a cytoplasmic bridge formed by the microtubules and the cytoplasm of the root cells. This bridge guides infection threads extending from the roots to the cortex of the bacterial cells. Finally, the S. meliloti cells enter the cytoplasm of the root cells through endocytosis (1). S. meliloti transform atmospheric nitrogen into a form that may be utilized by the host in which they reside (12). Also, the S. meliloti is significant in that it leaves behind excess nitrogen in the soil which may potentially reduce the need for fertilizers (7). The S. meliloti genome was isolated and sequenced from nodules and soil primarily from host plants such as the Medicago (alfalfa and perennial and annual medics), Melilotus (sweet clover), and Trigonella (fenugreek) species (11). The detailed study of S. meliloti and other Rhizobia will further inform microbiologists about how these bacteria colonize root surfaces of their host and what mechanisms make-up the complex rhizobium-legume symbiotic relationship (12).

Genome structure

S. meliloti is a fast growing Rhizobium that has a moderately small genome size of 6.7 Million base pairs. The genome is still quite complex and is made up of three circular elements of DNA, also known as replicons (5). One is a single chromosome 3.65 Mb long, while the other two are megaplasmids 1.68 Mb and 1.35 Mb long a piece (7). Each replicon contributes to the bacteria's symbiosis with its host plant. The largest replicon is responsible for all the housekeeping genes of S. meliloti cells, in particular the genes responsible for metabolic pathways. Also, it carries the genes involved in plant interaction, responding to external stress, mobility, and chemotaxis. The second replicon, named pSymB, carries genes involved in nutrient uptake and effective invasion of the plant host. The third and smallest replicon, named pSymA, is responsible for the the nitrogen-fixing capabilities of the bacterium (5). All three chromosomal components have been sequenced by researchers from around the world.

Cell structure and metabolism

S. meliloti is an aerobic bacterium that can be found either living independently in soil or on the roots of leguminous plants (14). A single superoxide dismutase, coded for by the sodA gene, catalyses the formation of hydrogen peroxide and oxygen from superoxides (14). S. meliloti cells will encounter two strikingly different environments during their life time, the soil and the nodules formed on the roots of plants (4). In the soil there is a large abundance of manganese that the cell can use and undergo aerobiosis. However, in the nodules there is a very low concentration of free oxygen and manganese where as iron is abundant in this highly acidic environment (9). In such conditions, it is favorable for the S. meliloti cells to utilize an iron-substituted superoxide dismutatse (15). It is most probably because the S. meliloti cells transition from the aerobic cycle in the soil to the microaerobic cycle in the nodule environment that they developed a cambialistic superoxide dismutase (14).


S. meliloti and root cells of legumes share a symbiotic relationship in which the bacterial cells fix atmospheric nitrogen into a usable form by the root cells (12). In return the plant cells produce reduced carbon compounds that the S. meliloti can uptake as their carbon source. Among the several possible carbon sources available to the S. meliloti cells, dicarboxylic acids such as succinate, fumerate, and malate are preferred because of their involvement in nitrogen fixation (13). The oxidation of these compounds is essential for S. melioti cells to be able to fix atmospheric nitrogen into a usable form for leguminous plants. Using these compounds allows the bacterial cells to maintain a fast growth rate as well. The uptake of succinate in preference to other carbon sources is known as succinate-mediated catabolite repression and it varies from the catabolite repression in other bacteria (10). The exact molecular mechanisms of the succinate-mediated catabolite repression is yet to be cleared up. One key note to make about S. meliloti is that their carbon sources do not enter the Phosphate Transfer System because the cells have an incomplete PTS and thus enter through a transporter known as the DctA permease (13). The bacterial cells synthesize several polysaccharides including glycogen, cyclic Beta-glucans, and exopolysaccharides. The biosynthetic pathways utilized by the cells include the Entner-Doudoroff and pentose-phosphate pathways with glucose 6-phosphate serving key enzymatic purposes (13).

Ecology

As other soil bacteria, Sinorhizobium meliloti cells serve a significant role in the survival of many plant species, and they also make a large contribution to the environment as a whole (12). The atmosphere is made up of approximately 85% nitrogen and it is thus an essential element to most living organisms and their biological processes. However, nitrogen is present in the atmosphere in the form of dinitrogen (N2) which is unusable by most plants and animals (8). S. meliloti cells serve a very crucial role in the environment in that they form symbiotic relationships with leguminous plants and convert N2 into organic nitrogen. This mutual relationship benefits the plants by providing them a readily available source of a very essential nutrient.

Interestingly, S. meliloti is also capable of denitrification as well. Denitrification is the process of reducing nitrate and nitrite into N2 which is more abundant in the environment. S. meliloti is unique in that it is one of the first organisms to have a cluster of all four nitrogen oxide reductases (nap, nir, nor, nos) on the same chromosome (8). Denitrification can have hazardous effects such as a loss of biologically useful nitrogen, a build up of N2O as a byproduct which contributes to acidic rain, and a depletion of the ozone layer. However, denitrification conducted by S. meliloti cells can have positive effects as well if it is harnessed in the correct way. For example, the N2O produced by denitrification can serve as a green-house gas that traps heat. Also, microbial denitrification can contribute significantly to the purification of wastewater. Nitrogen-rich fertilizers have contributed to the pollution of ground water (7). This water is potentially hazardous to pregnant women and infants and thus scientists are considering using microbial denitrification in water treatment facilities to remove excess NO3 (8).

Pathology

Since Sinorhizobium meliloti is a nitrogen fixing soil bacteria, its primary purpose is to undergo reactions to assist plants. It does not have any pathogenic characteristics, rather it maintains a symbiotic relationship with leguminous plants and ultimately betters the environment (12). S. meliloti cells, however, do conduct denitrification in addition to nitrogen fixation, and this process has known side effects to the environment. As mentioned above, excess denitrification can deplete the environment of a usable nitrogen source, result in a build up of N2O which contributes to acidic rain, and deplete the ozone layer (8). Whether or not S. meliloti cells directly contribute negatively to the environment as a result of their denitrification still remains under investigation.

Application to Biotechnology

S. meliloti cells are currently being used by microbiologists to further study plants and nutrient composition in the wild. Using these bacterial cells as a technology to further research is an example of microbial ecology. By learning the details that involve plant/microbe interactions, researchers can determine the correlation between the presence of certain compounds and the ability of plants to take them up (4). However, studying nutrients near the root of plants can prove challenging. The nutrients are often readily taken up by microorganisms that reside in the root region and thus it is difficult to isolate the root region without changing nutrient distributions. The symbiotic relationship that S. meliloti and other Rhizobia share with legumes is being utilized by microbial ecologists to fix this issue (3). Bacterial cells are stained with dies that flouresce only in the presence of certain nutrients in the root or the soil. The biosensing bacteria are added to plants and they illuminate to indicate regions where particular nutrients are present(3). Such technology has indicated nutrients, their distributions, their depletion and their uptake around plant roots and in the soil. In particular, such biotechnology is used to study to what extent sugars, organic acids, and bulk carbon support the growth of bacteria in varying plant species.

In addition, currently a study is underway to investigate the usefulness of Sinorhizobium meliloti in purifying drinking water because of the denitrification that it undergoes to convert NO3 to N2 and N2O. If proven effective, S. meliloti cells would be used in water treatment facilities in addition to other filters (8).

Current Research

1) The Australian National University - Research School of Biological Sciences is currently evaluating the methods by which undifferentiated cells of plants undergo development and how plants respond to bacterial infection. This team of researchers claims to approach plant biology with both molecular biology as well as genetics. Sinorhizobium meliloti cells have a model relationship with the legume roots that they often reside on. The team is using this model interaction as the basis of their study in order to determine which specific genes, gene products, and signaling molecules regulate growth and development of the nodule meristem. By isolating novel peptide signal molecules that may act as regulators for proliferating meristemic cells, they may be able to manipulate plants for adaption to the Australian environment and even for the production of chemicals that are beneficial to human cells. Finally, the research team is investigating the genome of the microsymbiont S. meliloti cells in order to determine an overall metabolic framework for these cells. This bacteria can adjust to several lifestyles, either to that of the nutrient-poor soil, the plant rhizosphere, and the inside of root nodules. They aim to determine which proteins allow them to thrive under various conditions (14).

2) Recently, The National Laboratory of Plant Molecular Genetics, as well as other notable institutes in China, have investigated the specific genes of S. meliloti that contribute to its nitrogen fixation abilities. The Rhizobium nifA gene has been determined to be an activator of nitrogen fixation as it causes its effects in nodule bacteria. To further understand the effects of the Sinorhizobium meliloti nifA gene on Alfalfa plants, the cDNA-AFLP technique was implemented to monitor the changes in gene expression in nifA mutant nodules. The purpose of this investigation was to determine whether or not the S. meliloti nifA mutant causes a different gene expression profile from the wild type gene in Alfalfa nodules (6).

3) Dublin University is currently examining the mechanisms of siderophore-mediated iron acquisition by Sinorhizobium meliloti. In the root nodules of plants, there is a high abundance of iron and a very low pH. S. meliloti cells, as mentioned above, utilize an iron-substituted superoxide dismutase to obtain their source of oxygen. Sidereophores dissolve ions of Fe3+ and allow cells to take them up via active transport mechanisms. Researchers are interested in identifying and characterizing the membrane proteins that function in siderophore recognition and transport (9).

References

1. Ampe, F., Kiss, E., Sabourdy, F., and Batut, J., “Transcriptome analysis of Sinorhizobium meliloti during symbiosis”, Genome Biology, 4:R15 doi:10.1186/gb-2003-4-2-r15, 2003, http://genomebiology.com/2003/4/2/R15

2. Barnett, MJ et al., "A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.", Proc Natl Acad Sci U S A, 2004 Nov 23;101(47):16636-41 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=19

3. Bringhurst, R. M., Cardon, Z., and Gage D. J., "Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor". Proc. Nat. Acad. Sci. 98:4540-4545, 2001 http://web.uconn.edu/gage/Notes/Publications/2001-biosensor%20PNAS%2098-4540.pdf

4. Djordjevic, M. A., "Sinorhizobium meliloti metabolism in the root nodule: a proteomic perspective", Australian Research Council Centre of Excellence for Integrative Legume Research, (Vol. 4) (No. 7) 1859-1872, 2004 http://www.cababstractsplus.org/google/abstract.asp?AcNo=20043149371

5. Finan, T., Weidner, S., Wong, K., Buhrmester, J., Chain, P., Vorhölter, F., Hernandez-Lucas, I., Becker, A., Cowie, A., Gouzy, J., Golding, B., and Pühler, A., "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti" Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 17, 9889-9894, August 14, 2001 http://bioinfo.genopole-toulouse.prd.fr/annotation/iANT/bacteria/rhime/

6. Gong, Z., He, ZS., Zhu, JB., Yu, GQ., and Zou, HS., "Sinorhizobium meliloti nifA mutant induces different gene expression profile from wild type in Alfalfa nodules", 16: 818–829. doi: 10.1038/sj.cr.7310096, Sep 26 2006 http://www.nature.com/cr/journal/v16/n10/abs/7310096a.html

7. Hofmann-Reinert, B., "In symbiosis with alfalfa: The complex genome sequence of Sinorhizobium meliloti", Genome News Network, August 6, 2001, http://www.genomenewsnetwork.org/articles/08_01/Symbiosis.shtml

8. House, B., “Novel Methods of Manipulating The Sinorhizobium Meliloti Genome and Studying the Effects of Denitrification on symbiotic Nitrogen Fixation”, Washington State University, School of Molecular Biology, pg. 101-125, 2003, https://research.wsulibs.wsu.edu:8443/dspace/bitstream/2376/98/1/b_house_050103.pdf

9. Keogh D., Collins P., Cuiv P., "Iron Transport in Bacteria", Dublin City University, 2006, http://webpages.dcu.ie/~oconnelm/projects.html

10. Lambert, A., Osteras, M., Mandon, K., Poggi, M C., Le Rudulier, D., "Fructose uptake in Sinorhizobium meliloti is mediated by a high-affinity ATP-binding cassette transport system", International Bibliographic Information on Dietary Supplements, 183(16): 4709-17, Auguest 2001, http://grande.nal.usda.gov/ibids/index.php?mode2=detail&origin=ibids_references&therow=447491

11. Marina L. Roumiantseva, Evgeny E. Andronov, Larissa A. Sharypova, Tatjana Dammann-Kalinowski, Mathias Keller, J. Peter W. Young, and Boris V. Simarov, "Diversity of Sinorhizobium meliloti from the Central Asian Alfalfa Gene Center", Applied and Environmental Microbiology, 68(9): 4694–4697. doi: 10.1128/AEM.68.9.4694-4697.2002, September 2002, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=124126

12. Milcamps, A., Struffi, P., and de Bruijn, F., "The Sinorhizobium meliloti Nutrient-Deprivation-Induced Tyrosine Degradation Gene hmgA Is Controlled by a Novel Member of the arsR Family of Regulatory Genes", Applied and Environmental Microbiology, 67(6): 2641–2648, doi: 10.1128/AEM.67.6.2641-2648.2001, June 2001, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=92919

13. Portais, J., Tavernier, P., Gosselin, I., Barbotin, J., "Cyclic organization of the carbohydrate metabolism in Sinorhizobium meliloti", European Journal of Biochemistry, 265 (1), 473–480. doi:10.1046/j.1432-1327.1999.00778.x, October 1999, http://www.blackwell-synergy.com/doi/full/10.1046/j.1432-1327.1999.00778.x?prevSearch=allfield%3A%28Sinorhizobium+meliloti%29&cookieSet=1

14. Rolfe, B., "Genomic Interactions", Australian Research Council Centre of Excellence for Integrative Legume Research, 12 March 2007, http://www.rsbs.anu.edu.au/ResearchGroups/GIG/index.php

15. Santos, R., Bocquet, S., Puppo, A., and Touati, D., "Characterization of an Atypical Superoxide Dismutase from Sinorhizobium meliloti", Journal of Bacteriology, 181(15): 4509–4516, 1999 August, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=103580


Edited by Muna Beg, a student of Rachel Larsen

Edited by KLB