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Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile

View Article: PubMed Central - PubMed

ABSTRACT

The motile mechanism of Mycoplasma mobile remains unknown but is believed to differ from any previously identified mechanism in bacteria. Gli349 of M. mobile is known to be responsible for both adhesion to glass surfaces and mobility. We therefore carried out sequence analyses of Gli349 and its homolog MYPU2110 from M. pulmonis to decipher their structures. We found that the motif “YxxxxxGF” appears 11 times in Gli349 and 16 times in MYPU2110. Further analysis of the sequences revealed that Gli349 contains 18 repeats of about 100 amino acid residues each, and MYPU2110 contains 22. No sequence homologous to any of the repeats was found in the NCBI RefSeq non-redundant sequence database, and no compatible fold structure was found among known protein structures, suggesting that the repeat found in Gli349 and MYPU2110 is novel and takes a new fold structure. Proteolysis of Gli349 using chymotrypsin revealed that cleavage positions were often located between the repeats, implying that regions connecting repeats are unstructured, flexible and exposed to the solvent. Assuming that each repeat folds into a structural domain, we constructed a model of Gli349 that fits well the shape and size of images obtained with electron microscopy.

No MeSH data available.


The degree of residue conservation at each position in the repeat is shown as information content. The information content of amino acid residue “a” at position “i” is calculated by the equation, I(a, i)=−p(a, i) log2p(a, i), where p(a, i) is the fractional content comprised by an amino acid residue.  at each position. As  becomes larger, the position “i” is regarded as more conserved. The three black bars indicate well conserved regions.
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f4-1_33: The degree of residue conservation at each position in the repeat is shown as information content. The information content of amino acid residue “a” at position “i” is calculated by the equation, I(a, i)=−p(a, i) log2p(a, i), where p(a, i) is the fractional content comprised by an amino acid residue. at each position. As becomes larger, the position “i” is regarded as more conserved. The three black bars indicate well conserved regions.

Mentions: We calculated sequence identities among the repeats using pairwise alignments generated with clustalW21,22 and found them to fall in a range of 13.6∼36.2% for Gli349 and 11.3∼35.7% for MYPU2110. The degree of sequence conservation in each column of the MSA of the 40 repeats is shown in the form of a sequence logo25 in Fig. 4. The YGF motif is the most conserved region within repeats, and there are three regions having high information values: 1 to 8, 21 to 36 and 54 to 63 (Fig. 4). These regions all contain a binary pattern of hydrophobic and hydrophilic residues, suggesting that the regions form amphipathic β strands and are located on the surface of the protein. Note that, in addition to these regions, there are several conserved amino acid residues: Gly at 38, Ser or Thr at 50, Asn at 76, Tyr at 83, Phe at 117 and Ile at 119.


Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile
The degree of residue conservation at each position in the repeat is shown as information content. The information content of amino acid residue “a” at position “i” is calculated by the equation, I(a, i)=−p(a, i) log2p(a, i), where p(a, i) is the fractional content comprised by an amino acid residue.  at each position. As  becomes larger, the position “i” is regarded as more conserved. The three black bars indicate well conserved regions.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036628&req=5

f4-1_33: The degree of residue conservation at each position in the repeat is shown as information content. The information content of amino acid residue “a” at position “i” is calculated by the equation, I(a, i)=−p(a, i) log2p(a, i), where p(a, i) is the fractional content comprised by an amino acid residue. at each position. As becomes larger, the position “i” is regarded as more conserved. The three black bars indicate well conserved regions.
Mentions: We calculated sequence identities among the repeats using pairwise alignments generated with clustalW21,22 and found them to fall in a range of 13.6∼36.2% for Gli349 and 11.3∼35.7% for MYPU2110. The degree of sequence conservation in each column of the MSA of the 40 repeats is shown in the form of a sequence logo25 in Fig. 4. The YGF motif is the most conserved region within repeats, and there are three regions having high information values: 1 to 8, 21 to 36 and 54 to 63 (Fig. 4). These regions all contain a binary pattern of hydrophobic and hydrophilic residues, suggesting that the regions form amphipathic β strands and are located on the surface of the protein. Note that, in addition to these regions, there are several conserved amino acid residues: Gly at 38, Ser or Thr at 50, Asn at 76, Tyr at 83, Phe at 117 and Ile at 119.

View Article: PubMed Central - PubMed

ABSTRACT

The motile mechanism of Mycoplasma mobile remains unknown but is believed to differ from any previously identified mechanism in bacteria. Gli349 of M. mobile is known to be responsible for both adhesion to glass surfaces and mobility. We therefore carried out sequence analyses of Gli349 and its homolog MYPU2110 from M. pulmonis to decipher their structures. We found that the motif “YxxxxxGF” appears 11 times in Gli349 and 16 times in MYPU2110. Further analysis of the sequences revealed that Gli349 contains 18 repeats of about 100 amino acid residues each, and MYPU2110 contains 22. No sequence homologous to any of the repeats was found in the NCBI RefSeq non-redundant sequence database, and no compatible fold structure was found among known protein structures, suggesting that the repeat found in Gli349 and MYPU2110 is novel and takes a new fold structure. Proteolysis of Gli349 using chymotrypsin revealed that cleavage positions were often located between the repeats, implying that regions connecting repeats are unstructured, flexible and exposed to the solvent. Assuming that each repeat folds into a structural domain, we constructed a model of Gli349 that fits well the shape and size of images obtained with electron microscopy.

No MeSH data available.