Preliminary comparative analysis of the genomes of selected field reisolates of the Mycoplasma synoviae vaccine strain MS-H reveals both stable and unstable mutations after passage in vivo

Kordafshari, Somayeh; Shil, Pollob; Marenda, Marc S.; Olaogun, Olusola M.; Konsak-Ilievski, Barbara; Disint, Jillian; Noormohammadi, Amir H.

doi:10.1186/s12864-020-06995-z

Table 2 Homology modelling results of proteins vary between MS-H and its field isolates

From: Preliminary comparative analysis of the genomes of selected field reisolates of the Mycoplasma synoviae vaccine strain MS-H reveals both stable and unstable mutations after passage in vivo

Gene locus-tag	Percentage of residues modelled at > 90% confidence	Protein product in MS-H	Protein effect	Model template library ID	MS-H vs. isolates	Secondary structure prediction^a			Protein length (amino acid)	Mutational sensitivity ^b (potential functional/phenotypic effect)
Gene locus-tag	Percentage of residues modelled at > 90% confidence	Protein product in MS-H	Protein effect	Model template library ID	MS-H vs. isolates	α helix %	β strand %	Different structure	Protein length (amino acid)
MSH_RS00965	99	GTP-binding protein Obg	Non-conservative substitution	c1udxA	MS-H	26	26	Yes	424	Low
MSH_RS00965	99	GTP-binding protein Obg	Non-conservative substitution	c1udxA	MS-H4, MS-H5	29	26	Yes	424	Low
MSH_RS00965	99	GTP-binding protein Obg	Conservative substitution	c1udxA	MS-H	26	26	No	424	Medium
MSH_RS00965	99	GTP-binding protein Obg	Conservative substitution	c1udxA	101546-101731	26	26	No	424	Medium
MSH_RS01740	91	Peptide ABC transporter ATP-binding protein	Frameshift	c5ws4A	MS-H	31	24	Yes	156	High
MSH_RS01740	91	Peptide ABC transporter ATP-binding protein	Frameshift	c5ws4A	MS-H3, MS-H4- 101546-101731	68	7	Yes	796	High
MSH_RS01990	75	Cardiolipin synthetase	Non-conservative Substitution	c3hsiC	MS-H	50	17	Yes	504	High
MSH_RS01990	75	Cardiolipin synthetase	Non-conservative Substitution	c3hsiC	MS-H4	51	17	Yes	504	High
MSH_RS00995	0	Hypothetical protein	Non-conservative substitution	c2yu6A	MS-H	65	8	No	398	NA
MSH_RS00995	0	Hypothetical protein	Non-conservative substitution	c2yu6A	MS-H4	65	8	No	398	NA
MSH_RS01480	0	Hypothetical protein	Frameshift	d1r5qa	MS-H	_	_	_	166	NA
MSH_RS01480	0	Hypothetical protein	Frameshift	d1r8ja1	MS-H4	_	_	_	161	NA
MSH_RS01480	0	Hypothetical protein	Frameshift	d1r5qa	MS-H	_	_	_	166	NA
MSH_RS01480	0	Hypothetical protein	Frameshift	c3kblA	MS-H5	_	_	_	56	NA
MSH_RS01835	100	TatD family deoxyribonuclease	Non-conservative substitution	c3ipwA	MS-H	47	16	No	268	Low
MSH_RS01835	100	TatD family deoxyribonuclease	Non-conservative substitution	c3ipwA	MS-H4	47	16	No	268	Low
MSH_RS02805	100	S1 RNA-binding domain-containing protein	Non-conservative substitution	c2oceA	MS-H	55	10	Yes	705	Low
MSH_RS02805	100	S1 RNA-binding domain-containing protein	Non-conservative substitution	c2oceA	MS-H4	56	10	Yes	705	Low
MSH_RS01365	100	NAD-dependent glyceraldehyde -3-phosphate dehydrogenase	Conservative substitution	c3hq4R	MS-H	27	31	Yes	334	Low
MSH_RS01365	100	NAD-dependent glyceraldehyde -3-phosphate dehydrogenase	Conservative substitution	c3hq4R	101546	27	32	Yes	334	Low
MSH_RS02615	37	Hypothetical protein	Conservative substitution	c6dgvA	MS-H	55	7	No	651	Medium
MSH_RS02615	37	Hypothetical protein	Conservative substitution	c6dgvA	101546	55	7	No	651	Medium
MSH_RS02750	91	YbhB/YbcL family Raf kinase inhibitor-like protein	Conservative substitution	c2evvD	MS-H	6	23	No	221	High
MSH_RS02750	91	YbhB/YbcL family Raf kinase inhibitor-like protein	Conservative substitution	c2evvD	101546	6	23	No	221	High
MSH_RS02415	0	Hypothetical protein	Non-conservative substitution	c5il9A	MS-H	22	38	_	1575	NA
MSH_RS02415	0	Hypothetical protein	Non-conservative substitution		101546	_	_	_	1575	NA
MSH_RS01430	16	Hypothetical protein	Frameshift	c4aq4A	MS-H	36	12	Yes	797	Low
MSH_RS01430	16	Hypothetical protein	Frameshift	d1tdpa	101731	44	17	Yes	405	Low
MSH_RS01990	75	Cardiolipin synthetase	Conservative substitution	c3hsiC	MS-H	50	17	No	504	Low
MSH_RS01990	75	Cardiolipin synthetase	Conservative substitution	c3hsiC	101731	50	17	No	504	Low
MSH_RS02470	92	DNA-directed RNA polymerase subunit beta	Non-conservative substitution	c3lu0C	MS-H	33	25	No	1202	Low
MSH_RS02470	92	DNA-directed RNA polymerase subunit beta	Non-conservative substitution	c3lu0C	101731	33	25	No	1202	Low

^a “Yes” indicates different secondary structure of respective protein between MS-H and its reisolate/s; “No” shows that MS-H and its reisolate/s have the same secondary structure of the respective protein; “_” indicates that only a domain of respective protein was modelled and as the result the percentage of α helix and β strand were not reliable
^b “High” indicates that respective mutation highly likely has functional/phenotypic effect; “Medium” shows that respective mutation moderately likely has functional/phenotypic effect; “Low” shows that respective mutation has low potential functional/phenotypic effect; “NA” indicates that position corresponding to respective mutation was not modelled

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ISSN: 1471-2164

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