16S rRNA

Gary L. Hines

glhines@acm.org

This Web page is for those who want to make more sense of the Full Genome Sequence (FGS) results of their mitochondrial DNA (mtDNA). It concentrates on bases 1671-3229 of the mtDNA sequence, which code for the large subunit (16S) ribosomal RNA (rRNA).

After the rRNA is transcribed, it folds into a secondary structure of stems and loops, mostly following canonical (Watson-Crick, G-C and A-U) base-pairing, although there are some alternate base-pairings, such as G-U. (Note that the U base in RNA is coded as a T base in DNA. The tables below are showing the mtDNA.) The secondary structure given below is that published in Angela Burk, Emmanuel J. P. Douzery and Mark S. Springer, The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach, Journal of Mammalian Evolution, Vol. 9, No. 3, September 2002, 225-252.

Tables 1 through 33 below show the secondary structure, as given by Burk, Douzery and Springer (2002). The structure (stems and loops) and Cambridge Reference Sequence (CRS) sequence locations are given with representative sequences for several mammal species. Table 0 lists the species and GenBank numbers for the sequences:

Table 0

The sequences below are as given in Burk, Douzery and Springer (2002), except for chimp, gorilla, orangutan, cat, deer and pig. These were added by me, and any errors with them are entirely mine. I also am responsible for fiddling with the human secondary structure a little in Table 31 below.

The secondary structure can give you clues as to why your rRNA mutations may have occurred. For example, in Table 29 below, Stem 48 in the secondary structure forms the following shape, using the rCRS sequence:

A change from G to A at position 3010 has occurred independently in several different mtDNA haplogroups, and it is considered the founding mutation for the H1 haplogroup. To see why this change may have occurred more than once, notice that it changes the 3010-3027 base pairing from G-U to A-U:

In other words, this mutation changes the base pairing to the more favored canonical (Watson-Crick) A-U pairing.

The tables below also show whether your mutation is shared with another mammal species. For instance, 12 out of the 18 mammal species have an A-U pairing at the positions corresponding to human 3010-3027; 4 have a G-C pairing; and only human and chimp have a G-U pairing. That means people in the H1 haplogroup, and others with G3010A, have a "back mutation" at this locus that seems to work fine for most other mammal species.

I hope you can make similar discoveries about your rRNA using the tables below.

Table 1

Table 2

Table 3

Table 4

Table 5

Table 6

Table 7

Table 8

Table 9

Table 10

Table 11

Table 12

Table 13

Table 14

Table 15

Table 16

Table 17

Table 18

Table 19

Table 20

Table 21

Table 22

Table 23

Table 24

Table 25

Table 26

Table 27

Table 28

Table 29

Table 30

Table 31

Note: The Revised CRS (rCRS) deletes the 'C' at the original CRS position 3107 but retains the original numbering. The secondary structure model given by Burk, Douzery and Springer (2002) is based on the original CRS and includes the 'C' at 3107 as the last base in the 38' stem, followed by the 'T' at 3108 as the first base in the following loop. The 'A' at position 2711 in Table 23 causes a base pairing of A-C at this spot within the 38 stem.

In Table 31 I have omitted the 'C' at 3107 per the rCRS; position 3106 is followed by 3108, with the loop starting at 3109. This results in a canonical base pairing of A-T. Note that all of the other species in Table 31 have a canonical base pairing at this position as well (A-T or C-G).

Table 32

Table 33