User:Jarle Pahr/Organisms

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Name Type strain BSL GC % Genome size Characteristics
Mesoplasma florum ATCC 33453 1 27 793224 bp
Mesoplasma entomophilumATCC 43706


Contents

Mesoplasma florum

Key characteristics:

  • Small genome
  • Complex growth requirements
  • UGA encodes tryptophan, not stop codon.
  • Non-motile
  • Lacks amino acid and fatty acid biosynthesis (how much?).
  • Does not require sterol for growth, but may require polyoxyethylene sorbitan (Tween 80) in some media.

No defined minimal medium described yet? Metabolic analysis might lead to one? What compounds are required for growth?

Actually the same species as M.entomophilum, according to Tom Knight? (100% identical 16S rDNA regions).

Check out Weisburg et al. 1989. A Phylogenetic Analysis of the Mycoplasmas: Basis for Their Classification. http://jb.asm.org/content/171/12/6455.full.pdf+html

  • According to Weisburg 1989, the 16s RNA sequences for M. florum and M. entomophilum determined in that study were 99.7 % similar. However, only 70 % of the 16s RNA sequence of M. florum was determined. Only the sequence for M. entomophilum was deposited into GenBank (accession M23931). (1476 bp). Alignment of this sequence to the genome sequence of M. florum L1 by BLAST indicates that the two sequences may in fact be identical (all differences are due to gaps or non-called bases in the sequence determined by Weisburg, and both gaps are aligned to an uncalled base. These differences may thus plausibly be attributed to artefacts/errors in the sequencing performed by Weisburg et al.)
  • Related to the above: Volokhov et al. (2006) performed a study of 16S-23S rRNA spacer (ITS) region of Mollicutes species, including mesoplasma species. They write that "From these findings it can be concluded that when two species of the cluster show a 16S rRNA sequence similarity above 97%, they are likely to belong tothe same species." However, they continue with: " Our analysis of the 16S rRNA gene sequences of [some] species showed the existence of several pairs of Mollicutes species, which exhibit a high percent of homology. For example, [some pairs of mycoplasma species] have 99.2, 98.2, 99.9, and 99.7% nucleotide similarity between them, respectively. This finding additionally supports previous observations that 16S rRNA gene sequence analysis is not a sufficient genetic marker by itself for identification of the species." Regarding the ITS region they write that "The sequences obtained during this study and already published sequences showed very low character of intraspecies variability of the region. For example, low ITS sequence variations was found with 98-100% homologybetween sequences of several different mycoplasma strains".

Analysis based on data from Volokhov 2007:

Multiple alignment of ITS sequences from Mesoplasma florum strains W23, MQ-3 and L1 (GenBank accessions DQ004938, AY974065 and AY974064, respectively) show identical sequences, except the sequence from strain MQ-3 differing at one position (A instead of T) and having a single nucleotide insertion (T).

Alignment of the ITS sequences from strains TAC and W24 of Mesoplasma entomophilum (GenBank no. DQ004936 and DQ004937 respectively) show 100 % sequence identity. Alignment of the sequences from M. florum L1 and M. enomophilum again show 100 % sequence identity.

Figure 1 in Volokhov 2007 show M. florum and M. entophilum to be closely related, but with several other species in the same group (i.e, they do not form a separate branch, which might perhaps be expected if they were both (near)-identical and significantly different to the other closest related species).

Thus, both the 16S RNA gene and the 16S-24S ITS seem to be identical for Mesoplasma florum and Mesoplasma entomophilum.

Are there any other phylogenetic markers available for comparing the two?

From the data in Supplementary Table S5, Kolokhov 2007, it is found that for the RpoB gene, the nucleotide and amino acid similarities between entomophilum and florum are 95,6 % and 99,6 %, respectively. The other strains most similar to entomophilum have similarities of 95,1 94,7 94,2 91,9 (99,6 99,1 97,4 98,3) respectively.

Volokhov et al. write that "At the intraspecies level the nucleotide diversity of the rpoB and gyrB genes was found to be less than 2%". If taking this statement as fact, it may be argued that the data argue for entomophilum and florum to be considered separate species. At the very least, it is concluded that the genomes of the two organisms are not completely identical.

For the GyrB gene, the nucleotide and amino acid percent identities between florum and entomophilum are 95,6 and 99,2 %, respectively.

For an article dealing with reclassification of a Mesoplasma species, see http://ijs.sgmjournals.org/content/54/6/1951

For an article dealing with species classifcation by multi-locus/genome-wide sequence similarity, see Chan et al. 2012: http://www.biomedcentral.com/1471-2180/12/302

Chan et al. write that "analyses based on 16S rRNA gene sequences were not capable of delineating accepted species." and that " Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications."

They support a previous suggestion to use a 95 % average nucleotide identity as a cutoff value to define species.

Type strain: ATCC 33453: http://www.lgcstandards-atcc.org/products/all/33453.aspx?geo_country=no

Description from McCoy 1984:

"Cells pass through filters having 0.45-um pores, but most ,are retained on filters having 0.22-um pores. Colonies on agar are umbonate. Cultures are resistant to penicillin, and no reversion to walled forms occurs in the absence of penicillin. No growth response occurs when supplementary choles- terol is added."

"All three strains fermented glucose but not mannose, did not hydrolyze esculin or arbutin, did not produce carotenoid pigments, did not hydrolyze arginine or urea,and did not liquefy coagulat ed serum or hemadsorb guinea pigerythrocytes."

"Broth cultures of strains PP2, LIT, and GF1 grew rapidly, producing heavy turbidity in 18 h in MC broth, serum fraction broth, or serum-free Tween 80 broth."

"The guanine-plus-cytosine contents of the DNAs of the three acholeplasma strains averaged 27.3 plus minus 1 mol%"

"Carotenes are not produced, nor is B-D-glucosidase."

Resources:

http://www.straininfo.net/taxa/5955

Proteome: http://hamap.expasy.org/proteomes/MESFL.html

Sequence: http://microbes.ucsc.edu/cgi-bin/hgGateway?db=mesoFlor_L1

http://www.ncbi.nlm.nih.gov/nuccore/AE017263

http://www.labome.org/species/cellular/mollicutes/mesoplasma/mesoplasma-florum-2151.html

http://microbewiki.kenyon.edu/index.php/Mesoplasma_florum

http://bacmap.wishartlab.com/organisms/194

Mesoplasma florum database at Broad Institute: http://www.broadinstitute.org/annotation/microbes/mesoplasma_florum/

Mesoplasma florum at Center for Biological Sequence Analysis (CBS): http://www.cbs.dtu.dk/services/GenomeAtlas-2.0/show-genus.php?KLSO=ASC&KLSK=ORGANISMSORT&kingdom=Bacteria&KLphylaFirmicutes=on&kingdom=Bacteria&GLgenus=Mesoplasma&GLspecies=florum

Mesoplasma florum at biocyc: http://biocyc.org/MFLO265311/organism-summary?object=MFLO265311

Mesoplasma florum genome at Broad Institute: http://www.broadinstitute.org/annotation/genome/mesoplasma_florum.2

http://nashua.case.edu/PathwaysKegg/Web/?viewID=a418cc47-ab7e-46e4-a331-21fe82e40045&pwgid=78c070e6-a29e-416c-8f93-865d265798c8


Metabolic model: http://www.ebi.ac.uk/biomodels-main/BMID000000141045


Mesoplasma florum at Encyclopedia of Life (EoL): http://eol.org/pages/977375/overview

Stock collections:

http://www.hpacultures.org.uk/products/bacteria/detail.jsp?refId=NCTC%2011704&collection=nctc

Classification and discovery:

Acholeplasma florum, a New Species Isolated from Plants: http://ijs.sgmjournals.org/content/34/1/11.full.pdf

Revised Taxonomy of the Class Mollicutes: http://ijs.sgmjournals.org/content/43/2/378.full.pdf+html

"This designation requires the transfer of Acholephma florum (McCoy et al., 1984), Acholeplasma entomophilum (Tully et al., 1988), Acholeplasma seirertii(Bonnet et al., 1991), and Mycoplasma ktucae Rose et al., 1990)to Mesoplasma florum comb. nov., Mesoplasma entomophilum comb. nov., Mesoplasma seifertii comb. nov., and Mesoplasma luctucae comb.nov.,respectively"


Taxonomic Descriptions of Eight New Non-Sterol-Requiring Mollicutes Assigned to the Genus Mesoplasma :http://ijs.sgmjournals.org/content/44/4/685.long

Tully, J. G. 1983. Reflections on recovery of some fastidious mollicutes with implications of the changing host patterns of these organisms. Yale J.Biol. Med. 56:799-813. (Referenced in Tully 1993).

McCoy, Williams, and Thomas. 1979. Isolation of mycoplasmas from flowers, p. 75-80. In R. E. McCoy and H. Su (ed.), Mycoplasma disease of plants. Republic of China/United States Cooperative Science Seminar, National Science Council,Taipei, Republic ofChina.


Other (possibly) relevant publications:

Volokhov 2007. Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene. http://www.sciencedirect.com/science/article/pii/S1055790306004908


Sequencing of the intergenic 16S-23S rRNA spacer (ITS) region of Mollicutes species and their identification using microarray-based assay and DNA sequencing.: http://www.ncbi.nlm.nih.gov/pubmed/16470366

Article collection: (http://people.csail.mit.edu/tk/mfpapers/ (un/pw: meso/meso) ).

Mesoplasma florum riboswitch: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1999398/

Comparative metabolism of Mesoplasma, Entomoplasma, Mycoplasma, and Acholeplasma.: http://www.ncbi.nlm.nih.gov/pubmed/8863414

J Mol Microbiol Biotechnol. 2007;12(1-2):147-54. Regulation of carbon metabolism in the mollicutes and its relation to virulence.


Differential metabolism of Mycoplasma species as revealed by their genomes: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000200004

Phylogenetic relationships among members of the class Mollicutes deduced from rps3 gene sequences: http://ijs.sgmjournals.org/content/44/1/119.long


Evolution of the ssrA degradation tag in Mycoplasma: specificity switch to a different protease.:

Navas-Castillo, J., F. Laigret, A. Hocquellet, C. J. Chang, and J. M. BovC. Evidence for a phosphoenolpyruvate-dependent sugar-phosphotransferase system in the mollicute Achole- plasma florum. Biochimie.

Related presentations:

http://openwetware.org/images/2/20/SBWG-tk.pdf


Culturing:

Rose,Tully and Whitcomb. 1993. A test for measuring growth responses of mollicutes to serum and polyoxyethylene sorbitan. Int.J.Syst. Bacteriol.43527-532.

Conditions for growing Mycoplasma canadense and Mycoplasma verecundum in a serum-free medium.: http://aem.asm.org/content/56/7/2259.full.pdf

Other possible media: SM-1, M1D (complex). (Mentioned as growth medium for insect-derived acheloplasmas in http://ijs.sgmjournals.org/content/38/2/164.full.pdf+html)

Defined medium LD82 supported growth of Spiroplasmas. May this or a similiar medium also work for M. florum? http://aem.asm.org/content/46/6/1247.full.pdf

Medium G-199:

Cultivation of Mycoplasmas in a Modified Tissue Culture Medium: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169865/pdf/aem00005-0204.pdf

See also "Simplified media for spiroplasmas associated with tabanid flies"?

Grows in ATCC medium 1161 (http://www.atcc.org/~/media/DE32194753474A659F151E68B8BC8D04.ashx) according to http://openwetware.org/wiki/Mesoplasma_florum:Electroporation


Relevant? "Conditions for growing Mycoplasma canadense and Mycoplasma verecundum in a serum-free medium."

Genetic tools:

http://www.ncbi.nlm.nih.gov/pubmed/18832328 / http://parts.igem.org/Part:BBa_J70302

Protocols and media:


Characterization of Mycoplasmas by PCR and Sequence Analysis with Universal 16S rDNA Primers. in: Mycoplasma Protocols. Methods in Molecular Biology™ Volume 104, 1998, pp 145-165

Electroporation: http://openwetware.org/wiki/Mesoplasma_florum:Electroporation

Culture media: http://www.biolabprotocols.com/view/7153/Mesoplama-florum-Culture-media.html

PPLO medium: http://www.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/211456.pdf

Frey Mycoplasma broth: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/f6797dat.Par.0001.File.tmp/f6797dat.pdf

Frey broth: https://media.vwr.com/stibo/hi_res/8291701.pdf

Genomic DNA extraction: http://www.e-biotek.com/model-organisms/310-mesoplasma-florumgenomic-dna-.html?start=1

Persons and research groups involved in M florum research:

Mesoplasma entomophilum

Also known as Acheloplasma entomophilum

Identical to M. florum? (See above)

ATCC: http://www.lgcstandards-atcc.org/Products/All/43706.aspx?geo_country=no#97A3B80C25094AB18C0467A587FD7091

Description from. Tully et al. 1988:

"Cells are pleomorphic but primarily coccoid, varying from 300 to 800 nm in diameter. Cells lack true cell walls. Nonmotile. Colonies on solid medium containing 0.8% Noble agar usually have the appearance of fried eggs. Chemoorganotroph. Acid produced from glucose, but not mannose. Does not hydrolyze arginine, urea, or arbutin."

http://www.lgcstandards-atcc.org/Products/All/43706.aspx?geo_country=no

Tully JG, et al. Acholeplasma entomophilum sp. nov. from gut contents of a wide range of host insects. Int. J. Syst. Bacteriol. 38: 164-167, 1988. http://ijs.sgmjournals.org/content/38/2/164.full.pdf+html

http://www.straininfo.net/strains/355222

Acholeplasmas and similar nonsterol-requiring mollicutes from insects: missing link in microbial ecology. Curr. Microbiol. 13:ll-16.


See also http://www.mycoplasma-exp.com/hompag.htm

Culturing:

Grows in ATCC medium 988, SP-4: http://www.lgcstandards-atcc.org/~/media/D078A95CAFED4ADE877F47632F4E2EB5.ashx

M. genitalium

Arabidopsis thaliana

http://glowingplant.com/post/49878496390/how-to-grow-and-care-for-arabidopsis



E. coli

In LB medium, exponential phase has been estimated to end between OD600 0.6 - 1.0 (http://jb.asm.org/content/189/23/8746.full)


http://openwetware.org/wiki/F_plasmids


E. coli resources:


http://cgsc.biology.yale.edu/ColiLinks.php


Bibliography

No Gene-Specific Optimization of Mutation Rate in Escherichia coli: http://mbe.oxfordjournals.org/content/30/7/1559.full

Corynebacterium glucamicum

Bacillus subtilis

BacilloBricks: http://128.240.143.7:8082/

Lactobacillus acidophilus

Pseudomonas fluorescencs

Rhodococcus opacus

Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002219


Rhodococcus opacus strain PD630 as a new source of high-value single-cell oil? Isolation and characterization of triacylglycerols and other storage lipids: http://mic.sgmjournals.org/content/146/5/1143.full.pdf

RhodoCyc - an organism-specific database of metabolic pathways, compounds and reactions: http://rhodocyc.broadinstitute.org/

R. opacus comparative analysis: http://rhodocyc.broadinstitute.org/comp-genomics?tables=organism&tables=pathway&tables=tport&tables=tu&orgid=CGB1&orgid=NCF1&orgid=OPAG&orgid=REUTROPHA&orgid=SMAVER2&orgid=MTSMEG&orgid=RHA1&orgid=SMCOELV2&orgid=MTH37RVV2&orgids=%28CGB1+NCF1+OPAG+REUTROPHA+SMAVER2+MTSMEG+RHA1+SMCOELV2+MTH37RVV2+%29


Summary of Rhodococcus opacus reconstruction, version 14.5: http://rhodocyc.broadinstitute.org/RHOTITCHED/organism-summary

Rhodococcus Opacus strain B4 Path2models genome-scale metabolic model: http://www.ebi.ac.uk/biomodels-main/BMID000000141993


Escherichia coli

Mesoplasma florum

http://openwetware.org/wiki/Mesoplasma_florum

http://partsregistry.org/Mesoplasma_florum

http://microbewiki.kenyon.edu/index.php/Mesoplasma_florum

http://www.broadinstitute.org/annotation/genome/mesoplasma_florum

M. florum genome-scale model: http://biomodels.caltech.edu/BMID000000141045

Rhodococcus opacus

http://www.broadinstitute.org/blog/creature-feature-rhodococcus-opacus-pd630 http://mic.sgmjournals.org/content/146/5/1143.full.pdf

B. subtilis

http://bsubcyc.org/

C. glutamicum

Lactobacillus bulgaricus

http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus


In silico organisms

http://systemsbiology.ucsd.edu/Downloads

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