Mycobacterium avium subspecies paratuberculosis: Difference between revisions

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[[Image:Map_K10_genome.jpg|frame|none|left|Circular representation of the ''Map'' K-10 genome generated with GENESCENE software (DNAstar, Madison, WI). From inside: red arrow, rRNA operon; dark purple histogram, GC content; multicolored histogram, MAP ORFs coded according to functional classification; black arrows, 45 tRNAs; outer circle, scale. Image and caption credit and copyright: Li, et.al. [http://www.pnas.org/cgi/content/abstract/102/35/12344?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=mycobacterium+avium&searchid=1&FIRSTINDEX=0&volume=102&issue=35&resourcetype=HWCIT "The complete genome sequence of ''Mycobacterium avium'' subspecies ''paratuberculosis''"] [http://www.pnas.org/misc/rightperm.shtml ''PNAS''] ]]
[[Image:Map_K10_genome.jpg|frame|none|left|Circular representation of the ''Map'' K-10 genome generated with GENESCENE software (DNAstar, Madison, WI). From inside: red arrow, rRNA operon; dark purple histogram, GC content; multicolored histogram, MAP ORFs coded according to functional classification; black arrows, 45 tRNAs; outer circle, scale. Image and caption credit and copyright: Li, et.al. [http://www.pnas.org/cgi/content/abstract/102/35/12344?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=mycobacterium+avium&searchid=1&FIRSTINDEX=0&volume=102&issue=35&resourcetype=HWCIT "The complete genome sequence of ''Mycobacterium avium'' subspecies ''paratuberculosis''"] [http://www.pnas.org/misc/rightperm.shtml ''PNAS''] ]]


The ''Map'' strain used for sequencing, K-10, was originally isolated from a dairy herd in Wisconsin by investigators of the USDA National Animal Disease Center [10]. This strain is a typical bovine type II clinical isolate which was chosen because of its high efficiency of transformation with plasmid DNA [1], its virulence and its amenability to transposition mutagenesis. By random shotgun sequencing, 1.8- to 3.0-kb fragments were cloned into pUC18 and 66,129 sequences were used to create the final genome assembly. As represented in the figure, the K-10 ''Map'' genome has a single circular chromosome of 4,829,781 base pairs, 91.3% of which are protein coding. ''Map'' has a GC (guanine cytosine) content of 69.3%, an average gene density of 1,112 base pairs per gene and an average gene length of 1,015 base pairs per gene. This genome encodes 4,350 ORFs, 45 tRNAs and 1 rRNA operon. 39 protein sequences were found within the ''Map'' genome which have no identifiable homolog recorded as of yet. About 1.5% of the ''Map'' genome consists of repetitive DNA[7].  
The ''Map'' strain used for sequencing, K-10, was originally isolated from a dairy herd in Wisconsin by investigators of the USDA National Animal Disease Center [10]. This strain is a typical bovine type II clinical isolate which was chosen because of its high efficiency of transformation with plasmid DNA [1], its virulence and its amenability to transposition mutagenesis. By random shotgun sequencing, 1.8- to 3.0-kb fragments were cloned into pUC18 and 66,129 sequences were used to create the final genome assembly. As represented in the figure, the K-10 ''Map'' genome has a single circular chromosome of 4,829,781 base pairs, 91.3% of which are protein coding. ''Map'' has a GC (guanine cytosine) content of 69.3%, an average gene density of 1,112 base pairs per gene and an average gene length of 1,015 base pairs. This genome encodes 4,350 ORFs, 45 tRNAs and 1 rRNA operon. 39 protein sequences were found within the ''Map'' genome which have no identifiable homolog recorded as of yet. About 1.5% of the ''Map'' genome consists of repetitive DNA[7].  


Of the 19 insertion sequences identified in the K-10 genome, most represent homologs of other ''Mycobacterium'' IS elements. ''IS_MAP02'' and ''IS_MAP04'' are of interest because they have no homologs in other mycobacteria and thus could possibly be used as specific diagnostic targets for ''Map''. The ''Map'' genome encodes for all proteins involved in the following metabolic pathways which are used within the cell: glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the glyoxalate cycle. Also, the large number of genes for regulatory function found within the genome is consistent with ''Map''’s ability to survive in a wide range of environmental conditions. One major difference between ''Map'' and other mycobacteria is its inability to produce mycobactin ''in vitro'', which is a siderophore responsible for the binding and transport of iron into the cell. A sequence comparison of the mycobactin gene cluster between ''Map'' K-10, ''M. avium'' strain 104 and ''M. tuberculosis'' strain H37Rv reveals a possible reason for this deficiency. Within this cluster, the mbtA gene is much shorter in ''Map'' than the other two, lacking more than 200 residues important for protein function. Though this remains to be tested more thoroughly, this truncated domain may be the limiting factor in mycobactin production for ''Map'' since MbtA has been found to initiate siderophore synthesis. One additional ''Map'' genome feature to note is the extentsive functional redundancy; a result of gene duplication, this redundancy is based on amino acid content and is usually high among genes involved in lipid metabolism and oxidoreduction [7]. A greater concentration proteins for lipid metabolism in ''Map'' compared to other species may reflect its requirement of a robust cell wall which allows it to survive and colonize in the ruminant intestine [9].
Of the 19 insertion sequences identified in the K-10 genome, most represent homologs of other ''Mycobacterium'' IS elements. ''IS_MAP02'' and ''IS_MAP04'' are of interest because they have no homologs in other mycobacteria and thus could possibly be used as specific diagnostic targets for ''Map''. The ''Map'' genome encodes for all proteins involved in the following metabolic pathways which are used within the cell: glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the glyoxalate cycle. Also, the large number of genes for regulatory function found within the genome is consistent with ''Map''’s ability to survive in a wide range of environmental conditions. One major difference between ''Map'' and other mycobacteria is its inability to produce mycobactin ''in vitro'', which is a siderophore responsible for the binding and transport of iron into the cell. A sequence comparison of the mycobactin gene cluster between ''Map'' K-10, ''M. avium'' strain 104 and ''M. tuberculosis'' strain H37Rv reveals a possible reason for this deficiency. Within this cluster, the mbtA gene is much shorter in ''Map'' than the other two, lacking more than 200 residues important for protein function. Though this remains to be tested more thoroughly, this truncated domain may be the limiting factor in mycobactin production for ''Map'' since MbtA has been found to initiate siderophore synthesis. One additional ''Map'' genome feature to note is the extentsive functional redundancy; a result of gene duplication, this redundancy is based on amino acid content and is usually high among genes involved in lipid metabolism and oxidoreduction [7]. A greater concentration proteins for lipid metabolism in ''Map'' compared to other species may reflect its requirement of a robust cell wall which allows it to survive and colonize in the ruminant intestine [9].

Revision as of 11:09, 29 August 2007

A Microbial Biorealm page on the genus Mycobacterium avium subspecies paratuberculosis

Scanning electron micrograph of M. paratuberculosis. Image courtesy of Johne's Information Center, University of Wisconsin

.

Classification

Higher order taxa

Bacteria (Domain); Actinobacteria (Phylum); Actinobacteria (Class); Actinobacteridae (Subclass); Actinomycetales (Order); Corynebacterineae (Suborder); Mycobacteriaceae (Family); Mycobacterium (Genus); Mycobacterium avium complex (MAC) (Species group) [11]

Species

Mycobacterium avium

Subspecies

Mycobacterium avium subspecies paratuberculosis

Commonly referred to as MAP or Map

Also known as: Mycobacterium paratuberculosis, Mycobacterium johnei, Bacillus paratuberculosis, Bacterium paratuberculosis, Mycobacterium enteritidis, Darmtuberculose, and Mycobacterium avium paratuberculosis [11]

The classification of this organism has been subject to debate. Isolated over 100 years ago, it was originally termed Mycobacterium enteritidis chronicae pseudotuberculosae bovis johne [13]. Current classifications depend on genetic composition and phenotypic characteristics. With a genome almost identical to that of Mycobacterium avium (M. avium) and its subspecies, the International Association for Paratuberculosis has recognized the subspecies term (Map) as fitting. On the other hand, some researchers and organizations still use the name M. paratuberculosis, not only for simplicity, but as a result of its significant phenotypic variances from M. avium [3, 8].

Description and significance

M. paratuberculosis infection of J774 macrophages. Infected at a 30:1 ratio, macrophages are shown at 0 (A), 24 (B), 48 (C), and 72 (D) hours. During this time, Map is shown being engulfed by the macrophage, and the inset (E) shows a detail of intracellular bacilli. Scale bars = 1 μm. Image credit and copyright: Bannantine JP and Stabel JR. 2002 Biomed Central Microbiology Open Access Article "Killing of Mycobacterium avium subspecies paratuberculosis within macrophages."

Mycobacterium avium subspecies paratuberculosis (Map) is the etiologic agent of Johne’s disease (pronounced “YO-nees” [8]) also known as paratuberculosis. It was first isolated by German scientists H.A. Johne and L. Frothingham over a century ago from diseased animals displaying inflammation of the ileum [13]. Johne’s disease, named for one of its finders, is a mammalian disease that resembles some clinical and pathological aspects of Crohn’s disease in humans [2], and which has become an increasingly relevant problem for cattle farmers and the economy worldwide. Map is found primarily in ruminants (cattle, sheep, goats, deer, antelope, bison, etc) and their three-chambered stomach relatives [3]. Johne’s disease has been studied extensively in dairy cattle, where it has been called one of the most serious diseases affecting these animals to date [4]. It is estimated that 20% of dairy herds and 8% of beef herds in the United States are infected [6], leading to a $1.5 billion loss for the cattle industry each year. Adding to this problem, Map has also been found to infect a variety of other wild animals, such as badger, fox, primates, rabbits, and swine [1]. Different strains of Map have been found equally distributed throughout the affected species (the same strain of bacteria is able to infect multiple types of animals), contributing to this wide host range and ease of transfer between species [8], all of which make the bacteria and disease very hard to keep track of. Also making Map hard to track is its long incubation period in host organisms. Though animals are infected at a young age, they don’t begin to show visible symptoms until adulthood, at which point they have reached the critical stages of disease and rarely survive [3, 5].

Map, an obligate intracellular pathogen, is a small (0.5 x 1.5 micron [3]), rod shaped bacteria which grows in circular colonies reaching about 1-2 mm in diameter [13]. It is usually found to be off-white or yellow depending on the medium [3], and has the ability to adapt easily to many environments. Map not only can evade host defenses and survive within phagosomal compartments for more than two weeks, but it has also been found to reprogram the pattern of gene expression of bovine macrophages to increase its chance of survival and pathogenesis within the host [1, 13]. Though it requires a suitable cell medium for growth, Map can survive in the environment well beyond its presence in an animal host, creating drastic problems for farmers trying to eradicate Johne’s disease from their herds.

Due to the steady increase of Map infection prevalence throughout cattle farms of the world and the economic impacts which result, methods of detecting Map from environmental cultures are currently being studied and may provide insight into the infection mechanisms of this pathogen and thus provide a basis for the development of drugs which may eradicate Johne’s disease altogether. Also, the close relation between characteristics of Johne’s disease in ruminants and Crohn’s disease in humans (a chronic inflammatory bowel disease) has created an ongoing debate of whether or not Map is a possible causative agent of this human disease as well. Though it has been fully sequenced, further functional characterization of the Map genome may solve this mystery between Map and Crohn’s by increasing our understanding of the molecular biology as well as the physiology, pathogenesis and host specificity of this bacterium [9].

Genome structure

Circular representation of the Map K-10 genome generated with GENESCENE software (DNAstar, Madison, WI). From inside: red arrow, rRNA operon; dark purple histogram, GC content; multicolored histogram, MAP ORFs coded according to functional classification; black arrows, 45 tRNAs; outer circle, scale. Image and caption credit and copyright: Li, et.al. "The complete genome sequence of Mycobacterium avium subspecies paratuberculosis" PNAS

The Map strain used for sequencing, K-10, was originally isolated from a dairy herd in Wisconsin by investigators of the USDA National Animal Disease Center [10]. This strain is a typical bovine type II clinical isolate which was chosen because of its high efficiency of transformation with plasmid DNA [1], its virulence and its amenability to transposition mutagenesis. By random shotgun sequencing, 1.8- to 3.0-kb fragments were cloned into pUC18 and 66,129 sequences were used to create the final genome assembly. As represented in the figure, the K-10 Map genome has a single circular chromosome of 4,829,781 base pairs, 91.3% of which are protein coding. Map has a GC (guanine cytosine) content of 69.3%, an average gene density of 1,112 base pairs per gene and an average gene length of 1,015 base pairs. This genome encodes 4,350 ORFs, 45 tRNAs and 1 rRNA operon. 39 protein sequences were found within the Map genome which have no identifiable homolog recorded as of yet. About 1.5% of the Map genome consists of repetitive DNA[7].

Of the 19 insertion sequences identified in the K-10 genome, most represent homologs of other Mycobacterium IS elements. IS_MAP02 and IS_MAP04 are of interest because they have no homologs in other mycobacteria and thus could possibly be used as specific diagnostic targets for Map. The Map genome encodes for all proteins involved in the following metabolic pathways which are used within the cell: glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the glyoxalate cycle. Also, the large number of genes for regulatory function found within the genome is consistent with Map’s ability to survive in a wide range of environmental conditions. One major difference between Map and other mycobacteria is its inability to produce mycobactin in vitro, which is a siderophore responsible for the binding and transport of iron into the cell. A sequence comparison of the mycobactin gene cluster between Map K-10, M. avium strain 104 and M. tuberculosis strain H37Rv reveals a possible reason for this deficiency. Within this cluster, the mbtA gene is much shorter in Map than the other two, lacking more than 200 residues important for protein function. Though this remains to be tested more thoroughly, this truncated domain may be the limiting factor in mycobactin production for Map since MbtA has been found to initiate siderophore synthesis. One additional Map genome feature to note is the extentsive functional redundancy; a result of gene duplication, this redundancy is based on amino acid content and is usually high among genes involved in lipid metabolism and oxidoreduction [7]. A greater concentration proteins for lipid metabolism in Map compared to other species may reflect its requirement of a robust cell wall which allows it to survive and colonize in the ruminant intestine [9].

Cell structure and metabolism

Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

Cow with clinical signs of Johne's disease. Image courtesy of Johne's Information Center, University of Wisconsin

.

How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

MAP and Crohn's Disease

Methods of Detection

Enter summaries of the most recent research here--at least three required

References

[ 1 ] Chacon, Ofelia; Bermudez, Luiz E.; and Barletta, Raul G. “Johne’s Disease, Inflammatory Bowel Disease, and Mycobacterium paratuberculosis.” Annual Reviews of Microbiology. 2004. 58: 329-63.

[ 2 ] Collins, Michael T. “Paratuberculosis: Review of present knowledge.” Acta veterinaria Scandinavica. 2003. 44: 217-221.

[ 3 ] Collins, Michael T. “Update on paratuberculosis: 1. Epidemiology of Johne’s disease and the biology of Mycobacterium paratuberculosis.” Irish Veterinary Journal. 2003. 56(11): 565-574.

[ 4 ] Cook, Kimberly L. and Britt, Jenks S. “Optimization of methods for detecting Mycobacterium avium subsp. paratuberculosis in environmental samples using quantitative, real-time PCR.” Journal of Microbiological Methods. 2007. 69: 154-160.

[ 5 ] Grant, Irene R. “Mycobacterium avium ssp. paratuberculosis in foods: current evidence and potential consequences.” International Journal of Dairy Technology. 2006. 59(2): 112-117.

[ 6 ] Jaravata, Carmela V.; Smith, Wayne L.; Rensen, Gabriel J.; Ruzante, Juliana; and Cullor, James S. “Survey of Ground Beef for the Detection of Mycobacterium avium paratuberculosis.” Foodborne Pathogens and Disease. 2007. 4(1): 103-106.

[ 7 ] Li, Lingling; Bannantine, John P.; Zhang, Qing; Amonsin, Alongkorn; May, Barbara J.; Alt, David; Banerji, Nilanjana; Kanjilal, Sagarika; and Kapur, Vivek. “The complete genome sequence of Mycobacterium avium subspecies paratubersulosis.” PNAS. 2005. 102(35): 12344-12349.

[ 8 ] Manning, Elizabeth J.B. “Mycobacterium avium subspecies paratuberculosis: a review of current knowledge.” Journal of Zoo and Wildlife Medicine. 2001. 32(3): 293-304.

[ 9 ] Marri, Pradeep Reddy; Bannantine, John P.; and Golding, Geoffrey B. “Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer.” FEMS Microbiology Reviews. 2006. 30(6): 906-925.

[ 10 ] NCBI. “Mycobacterium avium subsp. paratuberculosis K-10 k10 project at Univ. Minnesota.” Entrez Genome Project.

[ 11 ] NCBI. “Mycobacterium avium subsp. paratuberculosis.” Taxonomy Browser. <>

[ 12 ] Prantera, C. “Mycobacterium and Crohn’s disease: The endless story.” Digestive and Liver Disease. 2007. 39: 452-454.

[ 13 ] Rowe, M.T. and Grant, I.R. “Mycobacterium avium ssp. paratuberculosis and its potential survival tactics.” Letters in Applied Microbiology. 2006. 42: 305-311.

[ 14 ] Windsor, P. “Research into vaccination against ovine Johne’s disease in Australia.” Small Ruminant Research. 2006. 62: 139-142.

Edited by Kyla Holmes, student of Rachel Larsen