Difference between revisions of "Part:BBa K2912002"

 
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<partinfo>BBa_K2912002 short</partinfo>
 
<partinfo>BBa_K2912002 short</partinfo>
  
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Refractile inclusion bodies, known as R bodies, are produced by only a few species of bacteria. These inclusion bodies are highly insoluble protein ribbons, typically seen coiled into cylindrical structures within the cell. R-bodies are produced by Paramecium endosymbionts belonging to the genus Caedibacter. These intracellular bacteria confer upon their hosts a phenomenon called the killer trait. This is one of the DNA sequences for the R body locus (reb) from Caedibacter taeniospiralis.
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==2019 SZU-China==
  
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RebC may be involved in the modification process. Either methylation or the trimming of terminal amino acids would result in a change of migration within an SDS-polyacrylamide gel. The migration of these polypeptides does not reflect their predicted sizes, and anomalous migration patterns are seen when these polypeptides are electrophoresed in gels with different percentages of acrylamide, making it difficult to assess which processes might be involved in generating species with different molecular weights. A polypeptide as small as RebC is probably not capable of carrying out such posttranslational functions itself, but, by binding to RebA or RebB, it may induce conformational changes which allow host proteins to modify the proteins.  
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===Biology===
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Refractile inclusion bodies, known as R bodies, are produced by only a few species of bacteria. These inclusion bodies are highly insoluble protein ribbons, typically seen coiled into cylindrical structures within the cell. R-bodies are produced by Paramecium endosymbionts belonging to the genus Caedibacter. These intracellular bacteria confer upon their hosts a phenomenon called the killer trait. This is one of the DNA sequences for the R body locus (reb) from Caedibacter taeniospiralis.
  
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RebC is also necessary for the modification of RebB into six species with different pI values. At each stage of the polymerization process there are several species differing in pl. The type of posttranslational modification involved is unknown. Phosphorylation of the numerous Ser and Thr residues in RebB would result in different pIs. It is possible that as the subunits polymerize, the modified acidic residues are blocked by folding or are involved in the covalent linkages themselves. Thus, as polymerization proceeds, the R body complex becomes increasingly basic.
 
  
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Reb C may be involved in the modification process. Either methylation or the trimming of terminal amino acids would result in a change of migration within an SDS-polyacrylamide gel. The migration of these polypeptides does not reflect their predicted sizes, and anomalous migration patterns are seen when these polypeptides are electrophoresed in gels with different percentages of acrylamide, making it difficult to assess which processes might be involved in generating species with different molecular weights. A polypeptide as small as reb C is probably not capable of carrying out such posttranslational functions itself, but, by binding to rebA or rebB, it may induce conformational changes that allow host proteins to modify the proteins.
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 +
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Reb C is also necessary for the modification of rebB into six species with different pI values. At each stage of the polymerization process，there are several species differing in pl. The type of posttranslational modification involved is unknown. Phosphorylation of the numerous Ser and Thr residues in rebB would result in different pIs. It is possible that as the subunits polymerize, the modified acidic residues are blocked by folding or are involved in the covalent linkages themselves. Thus, as polymerization proceeds, the R body complex becomes increasingly basic. Moreover, rebC and rebB are necessary for the basic polymerization process.
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For more information, please see [https://parts.igem.org/Part:BBa_K2912017 BBa_K2912017-R-body.]
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===Sequence===
 
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===Usage and Biology===
 
===Usage and Biology===
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<partinfo>BBa_K2912002 parameters</partinfo>
 
<partinfo>BBa_K2912002 parameters</partinfo>
 
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==2022 SZU-China==
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=== Basic physical and chemical properties===
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Number of amino acids: 56
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Molecular weight: 6036.68
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Theoretical pI: 4.43
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Amino acid composition:
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Total number of negatively charged residues (Asp + Glu): 7
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Total number of positively charged residues (Arg + Lys): 2
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Atomic composition:
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Formula: C(251)H(394)N(72)O(89)S(6)Total number of atoms: 812
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Extinction coefficients:
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This protein does not contain any Trp residues. Experience shows that
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this could result in more than 10% error in the computed extinction coefficient.
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Extinction coefficients are in units of  M(-1) cm(-1), at 280 nm measured in water.
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Ext. coefficient    1490
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Abs 0.1% (=1 g/l)  0.247, assuming all pairs of Cys residues form cystines
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Ext. coefficient    1490
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Abs 0.1% (=1 g/l)  0.247, assuming all Cys residues are reduced
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Instability index:
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The instability index (II) is computed to be 41.37
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This classifies the protein as unstable.
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Aliphatic index: 59.46
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Grand average of hydropathicity (GRAVY): -0.254
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===Reference===
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[1]Koehler L, Flemming FE, Schrallhammer M. Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates. Eur J Protistol. 2019 Apr;68:108-120. doi: 10.1016/j.ejop.2019.02.002. Epub 2019 Feb 12. PMID: 30826731.
 +
 +
[1]Wang B, Lin YC, Vasquez-Rifo A, Jo J, Price-Whelan A, McDonald ST, Brown LM, Sieben C, Dietrich LEP. Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence. Nat Commun. 2021 Jul 29;12(1):4613. doi: 10.1038/s41467-021-24796-0. PMID: 34326342; PMCID: PMC8322103.
 +
 +
[3]Heruth DP, Pond FR, Dilts JA, Quackenbush RL. Characterization of genetic determinants for R body synthesis and assembly in Caedibacter taeniospiralis 47 and 116. J Bacteriol. 1994 Jun;176(12):3559-67. doi: 10.1128/jb.176.12.3559-3567.1994. PMID: 8206833; PMCID: PMC205544.
 +
 +
[4]Pond FR, Gibson I, Lalucat J, Quackenbush RL. R-body-producing bacteria.Microbiol Rev. 1989 Mar;53(1):25-67. doi: 10.1128/mr.53.1.25-67.1989. PMID:2651865; PMCID: PMC372716.
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[5] Winter MA, Guhr KN, Berg GM. Impact of various body weights and serumcreatinine concentrations on the bias and accuracy of the Cockcroft-Gaultequation. Pharmacotherapy. 2012 Jul;32(7):604-12. doi:10.1002/j.1875-9114.2012.01098.x. Epub 2012 May 10. PMID: 22576791.
 +
 +
[6]Matsuoka JI, Ishizuna F, Kurumisawa K, Morohashi K, Ogawa T, Hidaka M, SaitoK, Ezawa T, Aono T. Stringent Expression Control of Pathogenic R-body Productionin Legume Symbiont <i>Azorhizobium caulinodans</i>. mBio. 2017 Jul25;8(4):e0071517. doi: 10.1128/mBio.00715-17. PMID: 28743814; PMCID:PMC5527310.
 +
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[7]White DW, Tartaglia LA. Leptin and OB-R: body weight regulation by a cytokinereceptor. Cytokine Growth Factor Rev. 1996 Dec;7(4):303-9. doi:10.1016/s1359-6101(96)00040-8. PMID: 9023054.
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[8]Matsuoka JI, Ishizuna F, Ogawa T, Hidaka M, Siarot L, Aono T. Localization ofthe reb operon expression is inconsistent with that of the R-body production inthe stem nodules formed by Azorhizobium caulinodans mutants having a deletion of praR. J Gen Appl Microbiol. 2019 Sep 14;65(4):209-213. doi:10.2323/jgam.2018.09.003. Epub 2019 Feb 5. PMID: 30726794.

Latest revision as of 13:11, 11 October 2022


RebC may be involved in the modification process of forming the R bodies

2019 SZU-China

Biology

Refractile inclusion bodies, known as R bodies, are produced by only a few species of bacteria. These inclusion bodies are highly insoluble protein ribbons, typically seen coiled into cylindrical structures within the cell. R-bodies are produced by Paramecium endosymbionts belonging to the genus Caedibacter. These intracellular bacteria confer upon their hosts a phenomenon called the killer trait. This is one of the DNA sequences for the R body locus (reb) from Caedibacter taeniospiralis.


Reb C may be involved in the modification process. Either methylation or the trimming of terminal amino acids would result in a change of migration within an SDS-polyacrylamide gel. The migration of these polypeptides does not reflect their predicted sizes, and anomalous migration patterns are seen when these polypeptides are electrophoresed in gels with different percentages of acrylamide, making it difficult to assess which processes might be involved in generating species with different molecular weights. A polypeptide as small as reb C is probably not capable of carrying out such posttranslational functions itself, but, by binding to rebA or rebB, it may induce conformational changes that allow host proteins to modify the proteins.


Reb C is also necessary for the modification of rebB into six species with different pI values. At each stage of the polymerization process，there are several species differing in pl. The type of posttranslational modification involved is unknown. Phosphorylation of the numerous Ser and Thr residues in rebB would result in different pIs. It is possible that as the subunits polymerize, the modified acidic residues are blocked by folding or are involved in the covalent linkages themselves. Thus, as polymerization proceeds, the R body complex becomes increasingly basic. Moreover, rebC and rebB are necessary for the basic polymerization process. For more information, please see BBa_K2912017-R-body.

Sequence

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


2022 SZU-China

Basic physical and chemical properties

Number of amino acids: 56

Molecular weight: 6036.68

Theoretical pI: 4.43

Amino acid composition: Total number of negatively charged residues (Asp + Glu): 7 Total number of positively charged residues (Arg + Lys): 2

Atomic composition: Formula: C(251)H(394)N(72)O(89)S(6)Total number of atoms: 812

Extinction coefficients: This protein does not contain any Trp residues. Experience shows that this could result in more than 10% error in the computed extinction coefficient. Extinction coefficients are in units of M(-1) cm(-1), at 280 nm measured in water. Ext. coefficient 1490

Abs 0.1% (=1 g/l) 0.247, assuming all pairs of Cys residues form cystines Ext. coefficient 1490

Abs 0.1% (=1 g/l) 0.247, assuming all Cys residues are reduced Instability index:

The instability index (II) is computed to be 41.37 This classifies the protein as unstable.

Aliphatic index: 59.46

Grand average of hydropathicity (GRAVY): -0.254

Reference

[1]Koehler L, Flemming FE, Schrallhammer M. Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates. Eur J Protistol. 2019 Apr;68:108-120. doi: 10.1016/j.ejop.2019.02.002. Epub 2019 Feb 12. PMID: 30826731.

[1]Wang B, Lin YC, Vasquez-Rifo A, Jo J, Price-Whelan A, McDonald ST, Brown LM, Sieben C, Dietrich LEP. Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence. Nat Commun. 2021 Jul 29;12(1):4613. doi: 10.1038/s41467-021-24796-0. PMID: 34326342; PMCID: PMC8322103.

[3]Heruth DP, Pond FR, Dilts JA, Quackenbush RL. Characterization of genetic determinants for R body synthesis and assembly in Caedibacter taeniospiralis 47 and 116. J Bacteriol. 1994 Jun;176(12):3559-67. doi: 10.1128/jb.176.12.3559-3567.1994. PMID: 8206833; PMCID: PMC205544.

[4]Pond FR, Gibson I, Lalucat J, Quackenbush RL. R-body-producing bacteria.Microbiol Rev. 1989 Mar;53(1):25-67. doi: 10.1128/mr.53.1.25-67.1989. PMID:2651865; PMCID: PMC372716.

[5] Winter MA, Guhr KN, Berg GM. Impact of various body weights and serumcreatinine concentrations on the bias and accuracy of the Cockcroft-Gaultequation. Pharmacotherapy. 2012 Jul;32(7):604-12. doi:10.1002/j.1875-9114.2012.01098.x. Epub 2012 May 10. PMID: 22576791.

[6]Matsuoka JI, Ishizuna F, Kurumisawa K, Morohashi K, Ogawa T, Hidaka M, SaitoK, Ezawa T, Aono T. Stringent Expression Control of Pathogenic R-body Productionin Legume Symbiont Azorhizobium caulinodans. mBio. 2017 Jul25;8(4):e0071517. doi: 10.1128/mBio.00715-17. PMID: 28743814; PMCID:PMC5527310.

[7]White DW, Tartaglia LA. Leptin and OB-R: body weight regulation by a cytokinereceptor. Cytokine Growth Factor Rev. 1996 Dec;7(4):303-9. doi:10.1016/s1359-6101(96)00040-8. PMID: 9023054.

[8]Matsuoka JI, Ishizuna F, Ogawa T, Hidaka M, Siarot L, Aono T. Localization ofthe reb operon expression is inconsistent with that of the R-body production inthe stem nodules formed by Azorhizobium caulinodans mutants having a deletion of praR. J Gen Appl Microbiol. 2019 Sep 14;65(4):209-213. doi:10.2323/jgam.2018.09.003. Epub 2019 Feb 5. PMID: 30726794.