Small-subunit ribosomal RNA

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

Zarlenga, D.S., Lichtenfels, J.R. and Stringfellow, F. (1994a) Cloning and sequence analysis of the small subunit ribosomal RNA gene from Nematodirus battus. Journal of Parasitology 80, 342-344. 

S small subunit ribosomal RNA Small subunit of the 70S ribosome of... 

Telford, M.J., Lockyer, A.E., Cartwright-Finch, C. and Littlewood, D.T.J. (2003) Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms. Proceedings of the Royal Society of London Series B - Biological Sciences 2 70, 1 077-1 083. 

Wuyts, J., De Rijk, P., Van de Peer, Y., Pison, G., Rousseeuw, P. and De Wachter, R. (2000) Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in areaV4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Research 28, 4698 1708. 

Fig. 1.1.7. Selected Helix 45 motifs located at the 3 end of the small subunit ribosomal RNA. The successive dimethylated adenosines within the tetraloop are conserved in most organisms. The reason for the methylation is unclear (m62A is N6,N6-dimethyladenosine).

At first, trees depicting a symbiotic origin of mitochondria and chloroplasts were sketchy, and were cobbled together from partial sequences of diverse molecules, 5S RNA, ferredoxin, cytochrome c, based on very few organisms (Schwartz and Dayhoff 1978). They were easily criticized (Demoulin 1979). The decisive evidence came from systematic investigations of bacterial phylogeny based on comparisons of the small subunit ribosomal RNA (SSU rRNA) pioneered by the group led by Carl Woese at the University of Illinois. 

Sogin ML (1989b) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Am Zool 29 487-499... 

The 3 minor domain (domain IV) of the small subunit ribosomal RNA contains many elements which mediate interactions with other molecules during translation. However, despite the conservation of function within this domain, the homology between the plant 18 S rRNAs and E. coli small subunit RNA within this 3 region is limited.34,60,41 This segment within the E. coli molecule contains only 83 nucleotides as compared to 111 nucleotides for the four plant species examined. The additional nucleotides within the plant RNA have been constrained to conform to a... 

Throughout the 2003 mesocosm study, water (50-500 ml) was collected every third day onto 0.8 gm Supor membrane filters (Pall corp.) and stored at -80°C until analysis. Following enumeration of Phaeocystis sp. single cells and colonies, two samples were chosen for molecular determination of the composition of the Phaeocystis sp. community. Gene sequence analysis of Phaeocystis sp. small subunit ribosomal RNA (rRNA) genes from samples collected from a fertilized enclosure early in the experiment when only single cells were present (5 March 2003 single cells 15 ml"1,... 

Bhattacharya D, Elwood HJ, Goff LJ, Sogin ML Phylogeny of GracUaria lemaneiformis (Rhodophyta) based on sequence analysis of its small subunit ribosomal RNA coding region. JPhycol 1990 26 181-186. 

Castlebury LA, Domier LL Small subunit ribosomal RNA gene phylogeny of Plasmodiophora brassicae. Mycologia 1998 90 102-107. 

Scholin, C.A. et al.. Two distinct small subunit ribosomal RNA genes in the North American toxic... 

Xu DP, Sun P, Warren A, Noh JH, Choi DL, Shin MK, et aL Hiylogenetic investigations on ten genera of tintinnid cUiates (CUiophora Spirotrichea Tintinnida), based on small subunit ribosomal RNA gene sequences. J Eukaryot Microbiol... 

Pawlowski, J., Berney, C. (2003). Episodic evolution of nuclear small subunit ribosomal RNA gene in the stem-lineage of Foraminlfera. In Donoghue, P.C.J., Smith, M.P. (eds.), Telling the Evolutionary Time Molecular Clocks and The Fossil Record, pp. 107-118. Systematics Association special volume 66. London Taylor and Francis. 

Table 1 List of selected primers used to amplify small subunit ribosomal RNA used for DGGE. The target sites, sequences and specificity of the primers are shown. R (reverse) and F (forward) indicate the orientation of the primers. Y indicates C/T, W indicates A/T, M indicates A/C, R indicates A/G, S indicates C/G. A GC clamp (GC-rich sequence) is attached to the 5 -end of the forward primers to prevent complete dissociation... 

The accuracy of the folding algorithm was tested on a database of structures that contains four small subunit ribosomal RNAs (rRNA), four Group I introns, three Group II introns, and 41 transfer RNAs (tRNA). The rRNAs and Group II introns were folded in domains of less than 500 nucleotides (5). Table III summarizes the percent of correctly predicted base pairs for this version of the algorithm and the last... 

Rajendhran J, Gunasekaran P. Microbial phylogeny and diversity small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res. 2011 166 99-110. 

Cohen, B.L., Gawthrop, A.B., and Cavalier-Smith, T. (1998) Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences. Philosophical Transactions of the Royal Society London B, 353, 2039-2061. Freeman, G. (1993) Regional specification during embryogenesis in the articulate brachiopod Terebratalia. Developmental Biology, 160,196-213. 

---