COMPARATIVE STUDY OF OVERLAPPING GENES IN THE GENOMES OF MYCOPLASMA HOMINIS AND MYCOPLASMA PENETRANS
HTML Full TextCOMPARATIVE STUDY OF OVERLAPPING GENES IN THE GENOMES OF MYCOPLASMA HOMINIS AND MYCOPLASMA PENETRANS
Kandavelmani Angamuthu*1 and Shanmughavel Piramanayagam 2
DBT Bioinformatics Facility, Department of Bioinformatics 1, Research and Development Centre 2, Bharathiar University, Coimbatore – 641046, Tamil Nadu, India
ABSTRACT: Overlapping genes are pairs of adjacent genes whose coding regions are partially or entirely overlapping. Overlapping genes in prokaryotes are a means to minimize genome size and increase the density of genetic information. Overlapping genes play an important role in genome reduction of Mycoplasmas during the course of their degenerative evolution. In this study overlapping genes in the genomes of two obligatory human parasites, Mycoplasma hominis and Mycoplasma penetrans were extracted and systematically analyzed. Overlapping genes were classified into different categories based on their direction of transcription. Gene pairs that occur as overlapping in both the genomes, gene pairs that occur as overlapping in one genome but are split in the other genome were separated out and more closely analysed. The study revealed that most of the overlapping genes in these genomes are formed due to loss of a stop codon or frame shift. The present study also emphasizes the significance of overlapping genes in the evolution of these genomes.
Keywords: |
Obligatory parasites, Frame shift, Evolution
INTRODUCTION: Overlapping genes are pairs of adjacent genes whose coding regions are partially or entirely overlapping. Overlapping genes are a common occurrence in viruses, bacteria and mitochondria.
Overlapping genes have also been identified in various eukaryotic organisms including humans and systematic analysis methods have been developed 1, 2. Overlapping genes have evolved due to mutational bias towards deletion 3.
Evidence from previous studies show that most overlapping genes have originated as a result of stop codon deletion, by a point mutation at the stop codon or by the introduction of a near - end frameshift extending the protein translation till the next in-frame stop codon 4-6.
Overlapping genes are also found to evolve due to the acquisition of an upstream start codon by the downstream gene 7. Genomic overlaps in prokaryotes may be a result of evolutionary pressure to minimize genome size and increase the density of genetic information 8.
Overlapping genes have been suggested to have multiple functions such as regulation of gene expression, translational coupling and genome overprinting – a process of generating novel genes through accumulated mutations inside a pre – existing gene 9, 10.
Overlapping genes are more conserved between species than non-overlapping genes mostly because a mutation in the overlapping region causes changes in both genes 11, 12. Overlapping genes can be used as rare genomic markers to get insight into the phylogeny of the completely sequenced microbial genomes 13. Mycoplasmas, the obligatory parasites of humans, animals and plants seem to have evolved more rapidly than other bacteria since some highly variable positions in their rRNA sequences are strongly conserved in other bacterial species 14.
Mycoplasmas have evolved from Gram-positive bacteria by reductive evolution thereby losing several genes involved in metabolism, cellular process and energy production 15, 16. However, overlapping genes have been proposed as means of achieving genome reduction by retaining indispensable genes and compressing maximum amount of information in available sequence space 17. As an endeavor to analyze the role of overlapping genes in genome reduction, in the present study all the overlapping genes in the genomes of the two obligatory human parasites, Mycoplasma hominis and Mycoplasma penetrans were systematically analyzed.
MATERIALS AND METHODS: The genome sequences of two obligatory human parasites, M. hominis and M. penetrans were downloaded from the National Center for Biotechnology Information website (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/).
Overlapping genes, defined as pairs of adjacent genes whose coding regions partly or completely overlap were extracted using the (CDS) annotation feature. The extracted overlapping gene pairs were classified into three directional patterns, namely, ‘convergent’ (→←), ‘unidirectional’ (→→, ←←), and ‘divergent’ (←→) based on their direction of transcription 18. The overlapping gene pairs of M.penetrans and M.hominis were furtherclassified into four categories,
(i) Gene pairs that occur as overlapping in both genomes
(ii) Gene pairs that overlap in both genomes with different number of overlapping bases
(iii)Gene pair that overlap in M. penetrans but are split in M. hominis
(iv)Gene pairs that overlap in M. hominis but are split in M. penetrans.
The gene name, function, direction of overlap and the number of overlapping bases were tabulated for each category an analysed 6.
RESULTS AND DISCUSSION: The number overlapping genes and their orientation in the genomes of M. hominis and M. penetrans are summarized in table 1. Most of the overlapping genes are unidirectional, a few pairs are convergent and only one gene pair in M. hominis is divergent. These results concur with the earlier hypothesis that most overlapping gene pairs have unidirectional structure 19. This is a common occurrence in prokaryote genomes because in prokaryotes adjacent genes with the same orientation are often organized into operons or clusters and are transcribed together in the same direction.
It has been previously reported that the number of overlapping genes increases with the genome size and the number of ORFs 5. In contrast to this notion, in the current study it is observed that M. penetrans with a comparatively larger genome size and higher number of genes is found to have lesser number of overlapping gene pairs than that of M. hominis (Table 1). It has been reported earlier that Mycoplasma genitalium with the smallest genome has the largest proportion of overlapping gene pairs 6. This clearly proves that overlapping genes play an important role in genome compaction of the minimal genomes of Mycoplasmas during their course of degenerative evolution.
TABLE 1: NUMBER OF OVERLAPPING GENE PAIRS AND THEIR ORIENTATION
Genome Size (Mb) | No. of Genes | No. of Overlapping gene pairs | % of Overlapping genes | Orientation of overlapping gene pairs | ||||
Unidirectional | Convergent | Divergent | ||||||
←← | →→ | →← | ← → | |||||
M. hominis | 0.67 | 577 | 111 | 19.2 | 45 | 61 | 4 | 1 |
M. penetrans | 1.36 | 1069 | 109 | 10.1 | 52 | 51 | 6 | 0 |
Overlapping genes, number of overlapping nucleotides (length) and their direction of overlap in the genomes of M. hominis and M. penetrans are listed in table 2 & 3 respectively. Among all the unidirectional overlapping gene pairs 35 pairs in M. hominis and15 pairs M. penetrans overlap only by one base. Most of the overlapping genes in M. hominis and M. penetrans are formed due to loss of a stop codon or frame shift.
Table 4 summarizes the gene pairs that are found to be overlapping in both the genomes. All the 12 common overlapping gene pairs are found to have unidirectional orientation.
Among the 12 common overlapping gene pairs, five gene pairs overlap by the same number of nucleotides.
Whereas, seven other common overlaps differ in their overlapping lengths. The five common unidirectional overlapping gene pairs are found on the same strand in both the genomes except for MHO_1230: MHO_1240 (→→) and MYPE7420: MYPE7430 (←←). There are 36 gene pairs that are overlapping in M. hominis but are non-overlapping in M. penetrans (Table 5). Whereas on the other hand, there are 17 gene pairs that are overlapping in M. penetrans but are split in M. hominis which has a smaller genome(Table 6). These discrepancies are in accordance with the notion that overlapping genes may be a means of compressing maximum amount of information into the available short sequence space may be a result of evolutionary pressure to minimize the genome size and increase the density of genetic information 20.
TABLE 2: OVERLAPPING GENES IN M. HOMINIS
S. No. | Genes | Genes | Length | Direction |
1 | MHO_0010 | rnpA | 26 | ←← |
2 | dnaN | MHO_0060 | 1 | →→ |
3 | ksgA | MHO_0090 | 8 | ←← |
4 | MHO_0090 | MHO_0100 | 1 | ←← |
5 | MHO_0190 | atpB | 8 | →→ |
6 | atpA | atpG | 22 | →→ |
7 | atpD | atpC | 1 | →→ |
8 | scpA | scpB | 11 | →→ |
9 | scpB | rluC | 14 | →→ |
10 | gatC | gatA | 11 | →→ |
11 | gatA | gatB | 8 | →→ |
12 | gatB | MHO_0460 | 8 | →→ |
13 | MHO_0580 | MHO_0590 | 1 | →→ |
14 | cysS | MHO_0620 | 1 | →→ |
15 | MHO_0660 | fba | 17 | ←← |
16 | MHO_0740 | MHO_0750 | 1 | →→ |
17 | MHO_0750 | MHO_0760 | 59 | →→ |
18 | MHO_0840 | uvrC | 11 | →→ |
19 | rplk | rplA | 1 | →→ |
20 | MHO_0960 | recR | 1 | →→ |
21 | dnaH | MHO_1000 | 8 | →→ |
22 | thrS | trpS | 1 | ←← |
23 | MHO_1070 | MHO_1080 | 8 | →→ |
24 | MHO_1080 | MHO_1090 | 50 | →→ |
25 | nusB | tlyA | 17 | →→ |
26 | tlyA | nifS | 1 | →→ |
27 | nifS | nifU | 14 | →→ |
28 | nifU | mucB | 8 | →→ |
29 | mucB | MHO_1260 | 1 | →→ |
30 | alaS | MHO_1320 | 13 | →→ |
31 | MHO_1320 | MHO_1330 | 8 | →→ |
32 | MHO_1330 | MHO_1340 | 11 | →→ |
33 | MHO_1340 | greA | 1 | →→ |
34 | MHO_1400 | rluD | 2 | ← → |
35 | oppD | oppF | 8 | →→ |
36 | MHO_1570 | MHO_1580 | 1 | →→ |
37 | prfA | hemK | 1 | →→ |
38 | cmk | engA | 14 | →→ |
39 | MHO_1710 | MHO_1720 | 14 | ←← |
40 | oppB | oppC | 17 | →→ |
41 | tktA | MHO_1780 | 11 | ←← |
42 | ruvA | ruvB | 26 | →→ |
43 | hisS | aspS | 17 | →→ |
44 | dgk | hpt | 13 | →→ |
45 | cbiO1 | cbiO2 | 10 | →→ |
46 | cbiO2 | cbiQ | 8 | →→ |
47 | ligA | MHO_2010 | 24 | →← |
48 | MHO_2010 | MHO_2020 | 76 | ←← |
49 | MHO_2060 | pgsA | 11 | →→ |
50 | smf | nfo | 9 | →← |
51 | MHO_2190 | MHO_2200 | 8 | ←← |
52 | MHO_2330 | MHO_2340 | 20 | ←← |
53 | MHO_2370 | ribF | 1 | →→ |
54 | MHO_2450 | MHO_2460 | 1 | ←← |
55 | infA | map | 1 | ←← |
56 | map | adk | 10 | ←← |
57 | adk | secY | 7 | ←← |
58 | secY | rplO | 1 | ←← |
59 | rpsE | rplR | 1 | ←← |
60 | rplN | rpsQ | 8 | ←← |
61 | rpsQ | rpmC | 1 | ←← |
62 | rplP | rpsC | 23 | ←← |
63 | rpsC | rplV | 1 | ←← |
64 | rpsS | rplB | 1 | ←← |
65 | rplW | rplD | 1 | ←← |
66 | rplD | rplC | 1 | ←← |
67 | lspA | ileS | 11 | ←← |
68 | MHO_3080 | MHO_3090 | 14 | →→ |
69 | atpD | atpA | 1 | ←← |
70 | MHO_3140 | MHO_3150 | 8 | ←← |
71 | MHO_3150 | MHO_3160 | 23 | ←← |
72 | MHO_3170 | MHO_3180 | 20 | ←← |
73 | hsdS | hsdS | 23 | ←← |
74 | MHO_3280 | MHO_3290 | 1 | ←← |
75 | rnhB | MHO_3310 | 8 | ←← |
76 | MHO_3360 | MHO_3370 | 14 | →← |
77 | uvrA | MHO_3430 | 11 | ←← |
78 | MHO_3440 | MHO_3450 | 38 | ←← |
79 | gidB | prs | 26 | ←← |
80 | ldh | pgi | 8 | ←← |
81 | pgi | rpsA | 11 | ←← |
82 | pepF | apt | 1 | ←← |
83 | md2 | md1 | 8 | ←← |
84 | rpII | MHO_3930 | 20 | ←← |
85 | engB | gcp | 1 | ←← |
86 | gcp | MHO_3960 | 7 | ←← |
87 | MHO_3960 | MHO_3970 | 1 | ←← |
88 | MHO_4000 | rpmG | 1 | ←← |
89 | dnaE | polA | 14 | →→ |
90 | recD | pth | 1 | →→ |
91 | pth | tilS | 14 | →→ |
92 | MHO_4320 | ung | 11 | →← |
93 | MHO_4380 | gltX | 20 | ←← |
94 | potA | potB | 32 | →→ |
95 | potB | potC | 8 | →→ |
96 | MHO_4500 | MHO_4510 | 7 | →→ |
97 | pyrH | frr | 1 | →→ |
98 | MHO_4660 | MHO_4670 | 1 | →→ |
99 | plsX | rnc | 11 | →→ |
100 | MHO_4750 | MHO_4760 | 10 | →→ |
101 | MHO_4760 | MHO_4770 | 26 | →→ |
102 | MHO_4870 | sps1 | 8 | →→ |
103 | MHO_4950 | bcrA | 1 | →→ |
104 | bcrA | MHO_4970 | 23 | →→ |
105 | MHO_4970 | MHO_4980 | 8 | →→ |
106 | MHO_4980 | MHO_4990 | 23 | →→ |
107 | nusA | MHO_5260 | 7 | →→ |
108 | MHO_5260 | infB | 49 | →→ |
109 | infB | rbfA | 14 | →→ |
110 | MHO_5310 | MHO_5320 | 8 | →→ |
111 | MHO_5330 | MHO_5340 | 1 | ←← |
TABLE 3: OVERLAPPING GENES IN M. PENETRANS
S. No. | Genes | Genes | Length | Direction |
1 | spoU | MYPE240 | 10 | →→ |
2 | MYPE340 | MYPE350 | 32 | →→ |
3 | MYPE380 | scpB | 11 | →→ |
4 | MYPE400 | engB | 1 | →→ |
5 | MYPE430 | MYPE440 | 109 | →→ |
6 | MYPE450 | MYPE460 | 23 | →→ |
7 | MYPE490 | fmt | 40 | →→ |
8 | prfA | hemK | 35 | →→ |
9 | MYPE670 | MYPE680 | 35 | →→ |
10 | hrcA | MYPE720 | 26 | →→ |
11 | nusA | MYPE1100 | 8 | →→ |
12 | infB | rbfA | 17 | →→ |
13 | nfo | fur | 13 | →→ |
14 | MYPE1280 | MYPE1290 | 17 | →→ |
15 | MYPE1290 | MYPE1300 | 26 | →← |
16 | MYPE1300 | rluB | 11 | ←← |
17 | Lsp | MYPE1330 | 8 | ←← |
18 | MYPE1440 | pth | 8 | →→ |
19 | MYPE1460 | MYPE1470 | 7 | →→ |
20 | mucB | MYPE1500 | 11 | ←← |
21 | Efp | MYPE1590 | 1 | →→ |
22 | MYPE1590 | nusB | 11 | →→ |
23 | MYPE1610 | MYPE1620 | 11 | →→ |
24 | MYPE1620 | MYPE1630 | 38 | →→ |
25 | Dam | dam | 38 | →→ |
26 | MYPE1830 | ligA | 23 | →→ |
27 | MYPE1970 | dnaE | 23 | →→ |
28 | Fpg | MYPE2010 | 28 | →→ |
29 | MYPE2020 | MYPE2030 | 44 | →→ |
30 | gatA | gatB | 23 | →→ |
31 | MYPE2200 | MYPE2210 | 8 | ←← |
32 | engA | gpsA | 11 | →→ |
33 | MYPE2390 | MYPE2400 | 53 | →→ |
34 | MYPE2470 | MYPE2480 | 20 | →→ |
35 | ruvB | ruvA | 35 | ←← |
36 | MYPE2830 | MYPE2840 | 4 | →← |
37 | hprK | lgt | 14 | →→ |
38 | MYPE3040 | rpe | 4 | →← |
39 | MYPE3070 | MYPE3080 | 62 | →→ |
40 | mraW | MYPE3230 | 1 | →→ |
41 | MYPE3350 | dgkA | 8 | →→ |
42 | Era | MYPE3380 | 1 | →→ |
43 | glyS | dnaG | 11 | →→ |
44 | plsX | rnc | 26 | →→ |
45 | tpiA | pgm | 11 | →→ |
46 | MYPE4190 | MYPE4200 | 55 | →← |
47 | ulaA | tktA | 1 | →→ |
48 | tktA | MYPE4520 | 14 | →→ |
49 | MYPE4520 | MYPE4530 | 20 | →→ |
50 | MYPE4600 | MYPE4610 | 1 | →→ |
51 | MYPE4640 | MYPE4650 | 8 | →→ |
52 | MYPE4730 | MYPE4740 | 17 | →→ |
53 | MYPE4850 | MYPE4860 | 16 | →→ |
54 | MYPE4930 | MYPE4940 | 20 | ←← |
55 | hemN | miaA | 14 | ←← |
56 | pdhA | pdhB | 1 | →→ |
57 | oppC | oppB | 8 | ←← |
58 | MYPE5580 | MYPE5590 | 8 | ←← |
59 | MYPE5590 | MYPE5600 | 29 | ←← |
60 | MYPE5620 | MYPE5630 | 14 | ←← |
61 | MYPE5630 | gmk | 1 | ←← |
62 | MYPE5680 | MYPE5690 | 17 | ←← |
63 | glpQ | MYPE5760 | 8 | ←← |
64 | Htp | MYPE5820 | 1 | ←← |
65 | MYPE5870 | MYPE5880 | 1 | ←← |
66 | MYPE5880 | MYPE5890 | 1 | ←← |
67 | MYPE5890 | MYPE5900 | 35 | ←← |
68 | MYPE6010 | MYPE6020 | 17 | ←← |
69 | MYPE6320 | MYPE6330 | 17 | ←← |
70 | MYPE6440 | MYPE6450 | 20 | ←← |
71 | MYPE6495 | MYPE6500 | 35 | ←← |
72 | MYPE6600 | MYPE6610 | 11 | ←← |
73 | MYPE6610 | MYPE6620 | 8 | ←← |
74 | dhfR | thyA | 1 | ←← |
75 | thyA | folD | 14 | ←← |
76 | araD | sgaU | 20 | ←← |
77 | sgaU | ulaD | 26 | ←← |
78 | MYPE7375 | MYPE7380 | 53 | ←← |
79 | nifU | nifS | 14 | ←← |
80 | MYPE7570 | MYPE7580 | 38 | ←← |
81 | MYPE7680 | MYPE7690 | 16 | ←← |
82 | fruK | fruA | 47 | ←← |
83 | fruA | MYPE7770 | 11 | ←← |
84 | pyrB | pyrR | 1 | ←← |
85 | gidB | MYPE8000 | 14 | →→ |
86 | MYPE8090 | MYPE8100 | 8 | ←← |
87 | hsdR | hsdR | 50 | ←← |
88 | MYPE8350 | sigA | 20 | ←← |
89 | MYPE8510 | MYPE8520 | 16 | ←← |
90 | MYPE8530 | alaS | 17 | ←← |
91 | potA | potB | 32 | →→ |
92 | potB | potC | 8 | →→ |
93 | potC | MYPE8600 | 13 | →→ |
94 | MYPE8600 | gcp | 23 | →→ |
95 | MYPE8620 | MYPE8630 | 17 | →→ |
96 | MYPE8730 | oppF | 8 | ←← |
97 | MYPE9020 | cysS | 8 | ←← |
98 | truB | MYPE9290 | 4 | →← |
99 | metS | MYPE9390 | 8 | ←← |
100 | MYPE9420 | MYPE9430 | 4 | →← |
101 | MYPE9440 | MYPE9450 | 13 | ←← |
102 | MYPE9640 | MYPE9650 | 11 | ←← |
103 | cbiO | cbiO | 16 | ←← |
104 | MYPE9870 | MYPE9880 | 8 | ←← |
105 | MYPE9880 | MYPE9890 | 28 | ←← |
106 | rpmC | rplP | 14 | ←← |
107 | rplW | rplD | 1 | ←← |
108 | rplD | rplC | 1 | ←← |
109 | MYPE10380 | ksgA | 20 | ←← |
TABLE 4: OVERLAPPING GENE PAIRS COMMON TO BOTH M. HOMINIS AND M. PENETRANS
S. No. | Gene Name | Function | Locus | Length of Overlap | Direction of Overlap | |||
M.hom | M.pen | M.hom | M.pen | M.hom | M.pen | |||
1 | prfA:
hemK |
peptide chain release factor 1:
S-adenosylmethionine-dependent methyltransferase |
MHO_1600: MHO_1610 | MYPE650: MYPE660 |
1 | 35 | →
→ |
→
→ |
2 | infB:
rbfA |
translation initiation factor IF-2:
ribosome-binding factor A |
MHO_5270: MHO_5280 | MYPE1110: MYPE1120 | 14 | 17 | →
→ |
→
→ |
3 | gatA:
gatB |
aspartyl/glutamyl-tRNA amidotransferase subunit A: aspartyl/glutamyl-tRNA amidotransferase subunit B |
MHO_0440: MHO_0450 |
MYPE2100: MYPE2110 |
8 | 23 | →
→ |
→
→ |
4 | ruvB:
ruvA |
Holliday junction DNA helicase B:
holliday junction DNA helicase |
MHO_1850: MHO_1860 |
MYPE2780: MYPE2790 |
26 | 35 | →
→ |
←
← |
5 | plsX:
rnc |
putative glycerol-3-phosphate acyltransferase PlsX: ribonuclease III | MHO_4680: MHO_4690 | MYPE3640: MYPE3650 | 11 | 26 | →
→ |
→
→ |
6 |
oppC: oppB |
oligopeptide transport system permease protein oligopeptide transport system permease protein | MHO_1740: MHO_1750 | MYPE5540: MYPE5550 | 17 | 8 | →
→ |
←
← |
7 | nifU:
nifS |
nitrogen fixation protein NifU: aminotransferase NifS | MHO_1230: MHO_1240 | MYPE7420: MYPE7430 | 14 | 14 | →
→ |
←
← |
8 | PotA:
potB |
spermidine/putrescine transport ATP-binding protein: spermidine/putrescine transport system permease |
MHO_4450: MHO_4460 |
MYPE8570: MYPE8580 |
32 | 32 | →
→ |
→
→ |
9 | potB:
potC |
spermidine/putrescine transport system permease: spermidine/putrescine transport system permease Po | MHO_4460: MHO_4470 | MYPE8580: MYPE8590 | 8 | 8 | →
→ |
→
→ |
10 |
cbiO: cbiO
|
cobalt transporter ATP-binding subunit:
cobalt transporter ATP-binding subunit |
MHO_1970: MHO_1980 | MYPE9760: MYPE9770 | 10 | 16 | →
→ |
← ←
|
11 |
rplW: rplD
|
50S ribosomal proteinL23:
50S ribosomal protein L4 |
MHO_2960: MHO_2970 | MYPE1010:
MYPE1010 |
1 | 1 | ←
← |
←
← |
12 | rplD:
rplC |
50S ribosomal protein L4:
50S ribosomal protein L3 |
MHO_2970: MHO_2980 | MYPE10170:
MYPE1018 |
1 | 1 | ←
← |
←
← |
TABLE 5: GENE PAIRS THAT OVERLAP IN M. HOMINIS BUT ARE SPLIT IN M. PENETRANS
S. No. | Gene name | Function | Locus | Length | Direction |
1 | atpA:
atpG |
ATP synthase subunit alpha:
ATP synthase subunit gamma |
MHO_0240: MHO_0250 | 22 | →
→ |
2 | atpD:
atpC |
ATP synthase subunit beta:
ATP synthase subunit epsilon |
MHO_0260:
MHO_0270 |
1 | →
→ |
3 | scpA:
scpB |
segregation and condensation protein A: segregation and condensation protein B | MHO_0400: MHO_0410 | 11 | →
→ |
4 | scpB:
rluC |
segregation and condensation protein B: ribosomal large subunit pseudouridine synthase | MHO_0410:
MHO_0420 |
14 | →
→ |
5 | gatC:
gatA |
glutamyl- tRNA(gln)amidotransferase subunit C: glutamyl-tRNA(gln)amidotransferase subunit A | MHO_0420: MHO_0440 | 11 | →
→ |
6 | thrS:
trpS |
threonyl-tRNA synthetase: Tryptophanyl-tRNA synthetase | MHO_1050: MHO_1060 | 1 | ←
← |
7 | nusB:
tlyA |
N utilization NusB-like protein:
Hemolysin A |
MHO_1210: MHO_1220 | 17 | →
→ |
8 | tlyA:
nifS |
Hemolysin A: Nitrogen fixation protein NifS(aminotransferase | MHO_1220: MHO_1230 | 1 | →
→ |
9 | oppD:
oppF |
putative oligopeptide transport ATP-binding protein: putative oligopeptide transport ATP-binding protein | MHO_1540: MHO_1550 | 8 | →
→ |
10 | Cmk:
engA |
Cytidylate kinase:
GTP-binding protein engA |
MHO_1670: MHO_1680 | 14 | →
→ |
11 | hisS:
aspS |
Histidyl-tRNA synthetase:
Aspartyl-tRNA synthetase |
MHO_1870:
MHO_1880 |
17 | →
→ |
12 | Dgk:
hpt |
Deoxyguanosine kinase:
Hypoxanthine-guanine phosphoribosyltransferase (HGP... |
MHO_1930: MHO_1940 | 18 | →
→ |
13 | Smf:
nfo |
DNA processing protein smf:
Endonuclease IV |
MHO_2130: MHO_2140 |
9 | →
← |
14 | infA:
map |
translation initiation factor IF-1: methionine aminopeptidase (MAP) | MHO_2760: MHO_2770 | 1 | ←
← |
15 | Map:
adk |
methionine aminopeptidase (MAP): Adenylate kinase (ATP-AMP transphosphorylase) | MHO_2770: MHO_2780 | 10 | ←
← |
16 | Adk:
secY |
Adenylate kinase (ATP-AMP transphosphorylase):
Preprotein translocase secY subunit |
MHO_2780: MHO_2790 | 7 | ←
← |
17 | secY:
rplO |
Preprotein translocase secY subunit:
50S ribosomal protein L15 |
MHO_2790: MHO_2800 | 1 | ←
← |
18 | rplN:
rpsQ |
50S ribosomal protein L14:
30S ribosomal protein S17 |
MHO_2880: MHO_2890 | 8 | ←
← |
19 | rpsQ:
rpmC |
30S ribosomal protein S17:
50S ribosomal protein L29 |
MHO_2890: MHO_2900 | 1 | ←
← |
20 | rplP:
rpsC |
50S ribosomal protein L16:
30S ribosomal protein S3 |
MHO_2910: MHO_2920 |
23 | ←
← |
21 | rpsC:
rplV |
30S ribosomal protein S3:
50S ribosomal protein L22 |
MHO_2920: MHO_2930 | 1 | ←
← |
22 | rpsS:
rplB |
30S ribosomal protein S19:
50S ribosomal protein L2 |
MHO_2940: MHO_2950 | 1 | ←
← |
23 | lspA:
ileS |
lipoprotein signal peptidase:
Isoleucyl-tRNA synthetase |
MHO_3040: MHO_3050 |
11 | ←
← |
24 | atpD:
atpA |
ATP synthase subunit beta:
ATP synthase subunit alpha |
MHO_3120: MHO_3130 | 1 | ←
← |
25 | hsdS:
hsdS |
Type I restriction enzyme specificity protein:
Type I restriction enzyme specificity protein |
MHO_3220: MHO_3230 |
23 | ←
← |
26 | gidB:
prs |
methyltransferase gidB:
ribose-phosphate pyrophosphokinase |
MHO_3540: MHO_3550 | 26 | ←
← |
27 | Ldh:
pgi |
L-lactate dehydrogenase:
glucose-6-phosphate isomerase |
MHO_3580: MHO_3590 |
8 | ←
← |
28 | Pgi:
rpsA |
glucose-6-phosphate isomerase:
30S ribosomal protein S1
|
MHO_3590: MHO_3600 | 11 | ←
← |
29 | pepF:
apt |
Oligoendopeptidase F:
Adenine phosphoribosyl transferase |
MHO_3670: MHO_3680 | 1 | ←
← |
30 | md2:
md1 |
ABC transporter ATP binding protein:
ABC transporter ATP binding protein |
MHO_3820: MHO_3830 | 8 | ←
← |
31 | engB:
gcp |
putative GTP-binding protein engB:
O-sialoglycoprotein endopeptidase |
MHO_3940: MHO_3950 | 1 | ←
← |
32 | DnaE:
polA |
DNA polymerase III subunit alpha:
DNA polymerase I |
MHO_4120: MHO_4130 | 14 | →
→ |
33 | recD:
pth |
Exodeoxyribonuclease V subunit alpha: Peptidyl-tRNA hydrolase | MHO_4200: MHO_4210 | 1 | →
→ |
34 | Pth:
tilS |
Peptidyl-tRNA hydrolase:
tRNA(Ile)-lysidine synthase |
MHO_4210: MHO_4220 |
14 | →
→ |
35 | pyrH:
frr |
Uridylate kinase smbA:
ribosome recycling factor |
MHO_4600: MHO_4610 | 1 | →
→ |
36 | infB:
rbfA |
translation initiation factor IF-2:
ribosome-binding factor A |
MHO_5270: MHO_5280 | 14 | →
→
|
TABLE 6: GENE PAIRS THAT OVERLAP IN M. PENETRANS BUT ARE SPLIT IN M. HOMINIS
S. No. | Gene name | Function | Locus | Length | Direction | |
1 | nfo:
fur |
endonuclease IV:
ferric uptake regulation protein |
MYPE1190:
MYPE1200 |
13 | →
→ |
|
2 | Dam: dam | adenine-specific DNA methyltransferase: adenine-specific DNA methyltransferase | MYPE1780: MYPE1790 | 38 | →
→ |
|
3 | engA:
gpsA |
GTP-binding protein EngA:
NAD-dependent glycerol-3-phosphate dehydrogenase |
MYPE2290:
MYPE2300 |
11 | →
→ |
|
4 | hprK:
lgt |
HPr kinase/phosphorylase: prolipoprotein diacylglyceryl transferase | MYPE2990: MYPE3000 | 14 | →
→ |
|
5 | glyS:
dnaG |
glycyl-tRNA synthetase:
DNA primase |
MYPE3390: MYPE3400 | 11 | →
→ |
|
6 | tpiA:
pgm |
triose phosphate isomerase [Mycoplasma penetrans H: phosphoglyceromutase | MYPE3730: MYPE3740 | 11 | →
→ |
|
7 | ulaA:
tktA |
ascorbate-specific PTS system enzyme IIC: transketolase | MYPE4500:
MYPE4510 |
1 | →
→ |
|
8 | hemN:
miaA |
coproporphyrinogen III oxidase :
tRNA-isopentenyl pyrophosphate transferase |
MYPE5010:
MYPE5020 |
14 | ←
←
|
|
9 | pdhA:
pdhB |
Pyruvate dehydrogenase E1 component subunit alpha: pyruvate dehydrogenase E1 component subunit beta | MYPE5080:
MYPE5090 |
1 | →
→ |
|
10 | dhfR:
thyA |
dihyrofolatereductase:
thymidylate synthase |
MYPE6860:
MYPE6870 |
1 | ←
← |
|
11 | thyA:
folD |
thymidylate synthase: methylenetetrahydrofolate dehydrogenase | MYPE6870: MYPE6880 | 14 | ←
←
|
|
12 | araD:
sgaU |
L-ribulose-5-phosphate 4-epimerase:
L-xylulose 5-phosphate 3-epimerase
|
MYPE7160: MYPE7170 | 20 | ←
←
|
|
13 | sgaU:
ulaD |
L-xylulose 5-phosphate 3-epimerase:
3-keto-L-gulonate-6-phosphate decarboxylase |
MYPE7170: MYPE7180 | 26 | ←
←
|
|
14 | fruK:
fruA |
1-phosphofructokinase: PTS system fructose-specific IIABC component | MYPE7750: MYPE7760 | 47 | ←
←
|
|
15 | pyrB:
pyrR |
aspartate carbamoyltransferase catalytic subunit: pyrimidine regulatory protein PyrR | MYPE7890:
MYPE7900 |
1 | ←
←
|
|
16 | hsdR:
hsdR |
type I restriction-modification system R subunit: type I restriction-modification system R subunit. | MYPE8220: MYPE8230 | 50 | ←
←
|
|
17 | rpmC:
rplP |
ribosomal protein L29:
50S ribosomal protein L16 |
MYPE10100: MYPE10110 | 14 | ←
←
|
CONCLUSION: Computational comparative genomic analysis of M. hominis and M. penetrans has provided a breakthrough towards the understanding of the evolution of these genomes. It has been analyzed that there is no correlation between the genome size, number of genes and number of overlapping gene pairs. Most of the overlapping genes in M. hominis and M. penetrans are formed due to loss of a stop codon or frame shift.
The current study reveals the significance of overlapping genes in bringing about the genome compaction of Mycoplasmas during the course of reductive evolution.
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How to cite this article:
Angamuthu K and Piramanayagam S: Comparative study of overlapping genes in the genomes of Mycoplasma hominis and Mycoplasma penetrans. Int J Pharm Sci Res 2013: 4(9); 3504-3517. doi: 10.13040/IJPSR. 0975-8232.4(9).3504-17
All © 2013 are reserved by International Journal of Pharmaceutical Sciences and Research. This Journal licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Article Information
29
3504-3517
638KB
1005
English
IJPSR
Kandavelmani Angamuthu* and Shanmughavel Piramanayagam
Research and Development Centre, DBT Bioinformatics Facility, Department of Bioinformatics, Bharathiar University, Coimbatore – 641046, Tamil Nadu, India
kandavelmani@gmail.com
29 April, 2013
15 July, 2013
21 August, 2013
http://dx.doi.org/10.13040/IJPSR.0975-8232.4(9).3504-17
01 September, 2013