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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.


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Alignment scores of subsequences of 120 residues against the profile of repeat Set #3. Plotted are the scores at the center position of the subsequences of Gli349 (a) and MYPU2110 (b). Scores were calculated using HMMER19. The unit on the vertical axis is the negative logarithm of the E-value of the alignment. The bars above the line denote repeats detected by HMMER19. Most of the repeats were found to be in tandem form. For Gli349, experimentally determined chymotrypsin susceptible sites are shown by asterisks (a).
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f3-1_33: Alignment scores of subsequences of 120 residues against the profile of repeat Set #3. Plotted are the scores at the center position of the subsequences of Gli349 (a) and MYPU2110 (b). Scores were calculated using HMMER19. The unit on the vertical axis is the negative logarithm of the E-value of the alignment. The bars above the line denote repeats detected by HMMER19. Most of the repeats were found to be in tandem form. For Gli349, experimentally determined chymotrypsin susceptible sites are shown by asterisks (a).

Mentions: We then searched for subsequences of Gli349 and MYPU2110 that are distantly homologous to the repeats in Set #1. Using the knowledge that Gli349 is orthologous to MYPU21101,3,24, we conjectured that there might be a distantly homologous subsequence in Gli349 that could be aligned to one of the repeats in Set #1 of MYPU2110 and vice versa. In this way, we found an additional five repeats within Gli349 and two within MYPU2110. Then using the MSA of the 30 (23+7) subsequences prepared using clustal W, which we call Set #2, we searched for additional repeat subsequences, and a profile was built using the hidden Markov model with HMMER15. When a repeat search using this profile found new repeats, they and the repeats in Set #2 were aligned to build a new profile based on Set #2 (updating the profile), and then the procedure returned to the starting point in the cycle of iterations (see Fig. 2). The cycle was repeated until the alignment at the i-th iteration and the new alignment at the (i+1)-th iteration had the same alignment score. After seven iterations, we finally obtained additional repeats, three in Gli349 and four in MYPU2110, whose positions are shown in Table 2. This last repeat set containing 40 repeat sequences was called Set #3. The similarities of all the repeats in Set #3 were statistically significant (E-value of each repeat in Set #3 was smaller than 2.6×10−14 against the profile). And as shown in Fig. 3, the peaks of the alignment scores correspond well to the positions of the repeats. The scores were calculated using a 120-residue long window so that the window would contain the entire repeat. Hereafter, “repeat” denotes repeat sequences in Set #3.


Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile
Alignment scores of subsequences of 120 residues against the profile of repeat Set #3. Plotted are the scores at the center position of the subsequences of Gli349 (a) and MYPU2110 (b). Scores were calculated using HMMER19. The unit on the vertical axis is the negative logarithm of the E-value of the alignment. The bars above the line denote repeats detected by HMMER19. Most of the repeats were found to be in tandem form. For Gli349, experimentally determined chymotrypsin susceptible sites are shown by asterisks (a).
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Related In: Results  -  Collection

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f3-1_33: Alignment scores of subsequences of 120 residues against the profile of repeat Set #3. Plotted are the scores at the center position of the subsequences of Gli349 (a) and MYPU2110 (b). Scores were calculated using HMMER19. The unit on the vertical axis is the negative logarithm of the E-value of the alignment. The bars above the line denote repeats detected by HMMER19. Most of the repeats were found to be in tandem form. For Gli349, experimentally determined chymotrypsin susceptible sites are shown by asterisks (a).
Mentions: We then searched for subsequences of Gli349 and MYPU2110 that are distantly homologous to the repeats in Set #1. Using the knowledge that Gli349 is orthologous to MYPU21101,3,24, we conjectured that there might be a distantly homologous subsequence in Gli349 that could be aligned to one of the repeats in Set #1 of MYPU2110 and vice versa. In this way, we found an additional five repeats within Gli349 and two within MYPU2110. Then using the MSA of the 30 (23+7) subsequences prepared using clustal W, which we call Set #2, we searched for additional repeat subsequences, and a profile was built using the hidden Markov model with HMMER15. When a repeat search using this profile found new repeats, they and the repeats in Set #2 were aligned to build a new profile based on Set #2 (updating the profile), and then the procedure returned to the starting point in the cycle of iterations (see Fig. 2). The cycle was repeated until the alignment at the i-th iteration and the new alignment at the (i+1)-th iteration had the same alignment score. After seven iterations, we finally obtained additional repeats, three in Gli349 and four in MYPU2110, whose positions are shown in Table 2. This last repeat set containing 40 repeat sequences was called Set #3. The similarities of all the repeats in Set #3 were statistically significant (E-value of each repeat in Set #3 was smaller than 2.6×10−14 against the profile). And as shown in Fig. 3, the peaks of the alignment scores correspond well to the positions of the repeats. The scores were calculated using a 120-residue long window so that the window would contain the entire repeat. Hereafter, “repeat” denotes repeat sequences in Set #3.

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.


Related in: MedlinePlus