TY - JOUR
T1 - Secondary structure at the 3′ terminal region of RNA coliphages
T2 - Comparison with tRNA
AU - Adhin, Malti R.
AU - Alblas, Jacqueline
AU - van Duin, Jan
PY - 1990/8/27
Y1 - 1990/8/27
N2 - Secondary structure models for the 3′ non-coding region of the four groups of coliphage RNA are proposed based on comparative sequence analysis and on previously published data on the sensitivity of nucleotides in MS2 RNA to chemical modification and enzymes. We report the following observations. (1) In contrast to the coding regions, the structure at the 3′ terminus is characterized by stable regular helices. We note the occurrence of the loop sequences 5′-GUUCGC and 5′-CGAAAG, that are reported to confer exceptional stability to stem structures. These features are probably present to promote the segregation of mother and daughter strands during replication. (2) Comparison of homologous helices indicates that only those base pair substitutions are allowed that maintain the thermodynamic stability. (3) We have compared the structure of phage RNA with tRNA. Overall similarity is low, but one common element may exist. It is a quasi-continuous helix of 12 basepairs that could be the equivalent of the 12 basepair long coaxially stacked helix, formed by the TψC arm and the aminoacyl acceptor arm in tRNA. As in tRNA, this structure element starts after the fourth nucleotide from the 3′ end. (4) Phage RNA contains a large variable region of about 35 nucleotides bulging out from the quasi-continuous helix. We speculate that the variable loop in present-day tRNA could be the remnant of the variable region found in phage RNA. The variable region contains overlapping binding sites for the replicase enzyme and the maturation protein. This common binding site may serve as a switch from replication to packaging.
AB - Secondary structure models for the 3′ non-coding region of the four groups of coliphage RNA are proposed based on comparative sequence analysis and on previously published data on the sensitivity of nucleotides in MS2 RNA to chemical modification and enzymes. We report the following observations. (1) In contrast to the coding regions, the structure at the 3′ terminus is characterized by stable regular helices. We note the occurrence of the loop sequences 5′-GUUCGC and 5′-CGAAAG, that are reported to confer exceptional stability to stem structures. These features are probably present to promote the segregation of mother and daughter strands during replication. (2) Comparison of homologous helices indicates that only those base pair substitutions are allowed that maintain the thermodynamic stability. (3) We have compared the structure of phage RNA with tRNA. Overall similarity is low, but one common element may exist. It is a quasi-continuous helix of 12 basepairs that could be the equivalent of the 12 basepair long coaxially stacked helix, formed by the TψC arm and the aminoacyl acceptor arm in tRNA. As in tRNA, this structure element starts after the fourth nucleotide from the 3′ end. (4) Phage RNA contains a large variable region of about 35 nucleotides bulging out from the quasi-continuous helix. We speculate that the variable loop in present-day tRNA could be the remnant of the variable region found in phage RNA. The variable region contains overlapping binding sites for the replicase enzyme and the maturation protein. This common binding site may serve as a switch from replication to packaging.
KW - Helix stability
KW - Phage RNA
KW - tRNA comparison
UR - http://www.scopus.com/inward/record.url?scp=0024995737&partnerID=8YFLogxK
U2 - 10.1016/0167-4781(90)90150-Z
DO - 10.1016/0167-4781(90)90150-Z
M3 - Article
C2 - 2207136
AN - SCOPUS:0024995737
SN - 0167-4781
VL - 1050
SP - 110
EP - 118
JO - BBA - Gene Structure and Expression
JF - BBA - Gene Structure and Expression
IS - 1-3
ER -