Conserved Alternative Splicing in the 5'-Untranslated Region of the Muscle-Specific Enolase Gene. Primary Structure of mRNAs, Expression and Influence of Secondary Structure on the Translation Efficiency

We set up an alternative splicing system in vitro in which the relative amounts of two spliced RNAs, one containing and the other lacking a particular exon, were directly proportional to the length of an inverted repeat inserted into the flanking introns. We then used the system to measure the effect of intramolecular complementarity on alternative splicing in vivo. We found that an alternative splice was induced in vivo only when the introns contained more than approximately 50 nucleotides of perfect complementarity, that is, only when the secondary structure was much more stable than most if not all possible secondary structures in natural mRNA precursors. We showed further that intron insertions containing long complements to splice sites and a branch point inhibited splicing in vitro but not in vivo. These results raise the possibility that in cells most pre-mRNA secondary structures either are not maintained long enough to influence splicing choices, or never form at all.

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A new hybrid coding for protein secondary structure prediction based on primary structure similarity

Gene ◽

10.1016/j.gene.2017.03.011 ◽

2017 ◽

Vol 618 ◽

pp. 8-13 ◽

Cited By ~ 11

Author(s):

Zhong Li ◽

Jing Wang ◽

Shunpu Zhang ◽

Qifeng Zhang ◽

Wuming Wu

Keyword(s):

Secondary Structure ◽

Primary Structure ◽

Structure Prediction ◽

Secondary Structure Prediction ◽

Protein Secondary Structure ◽

Protein Secondary Structure Prediction ◽

Hybrid Coding ◽

Structure Similarity

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Identifying the origin of local flexibility in a carbohydrate polymer

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2102168118 ◽

2021 ◽

Vol 118 (23) ◽

pp. e2102168118

Author(s):

Kelvin Anggara ◽

Yuntao Zhu ◽

Giulio Fittolani ◽

Yang Yu ◽

Theodore Tyrikos-Ergas ◽

...

Keyword(s):

Secondary Structure ◽

Primary Structure ◽

Material Properties ◽

Single Linkage ◽

Chain Flexibility ◽

Carbohydrate Polymers ◽

Monomer Sequence ◽

Structures And Properties ◽

Local Flexibility ◽

Carbohydrate Polymer

Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, are the most abundant materials found in nature whose structures and properties have been characterized only at the submicrometer level. Here, by imaging single-cellulose chains at the nanoscale, we determine the structure and local flexibility of cellulose as a function of its sequence (primary structure) and conformation (secondary structure). Changing the primary structure by chemical substitutions and geometrical variations in the secondary structure allow the chain flexibility to be engineered at the single-linkage level. Tuning local flexibility opens opportunities for the bottom-up design of carbohydrate materials.

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Role of the 5′-untranslated region of mRNA in the synthesis of S-adenosylmethionine decarboxylase and its regulation by spermine

Biochemical Journal ◽

10.1042/bj3020765 ◽

1994 ◽

Vol 302 (3) ◽

pp. 765-772 ◽

Cited By ~ 21

Author(s):

L M Shantz ◽

R Viswanath ◽

A E Pegg

Keyword(s):

Secondary Structure ◽

Untranslated Region ◽

Fold Increase ◽

Negative Regulator ◽

Mrna Levels ◽

Coding Region ◽

Polyamine Biosynthesis ◽

Adenosylmethionine Decarboxylase ◽

Spermine Synthase ◽

Synthase Inhibitor

S-Adenosylmethionine decarboxylase (AdoMetDC), a rate-limiting enzyme in polyamine biosynthesis, is regulated by polyamines at the levels of both transcription and translation. Two unusual features of AdoMetDC mRNA are a long (320 nt) 5′-untranslated region (5′UTR), which is thought to contain extensive secondary structure, and a short (15 nt) open reading frame (ORF) within the 5′UTR. We have studied the effects of altering these elements on both the expression of AdoMetDC and its regulation by n-butyl-1,3-diaminopropane (BDAP), a spermine synthase inhibitor. Human AdoMetDC cDNAs containing alterations in the 5′UTR, as well as chimaeric constructs in which the AdoMetDC 5′UTR was inserted ahead of the luciferase-coding region, were transfected into COS-7 cells. Construct pSAM320, which contains all of the 5′UTR, the AdoMetDC protein-coding region and the 3′UTR, was expressed poorly (2-fold over the endogenous activity). Deletion of virtually the entire 5′UTR, leaving nt -12 to -1, increased expression 59-fold, suggesting that 5′UTR acts as a negative regulator. The same effect was seen when the 27 nt at the extreme 5′ end were removed (pSAM293, 47-fold increase), or when the internal ORF which is present in this region was destroyed by changing the ATG to CGA (pSAM320-ATG, 38-fold increase). The expression and regulation of pSAM44 (made by deleting nt -288 to -12), which has very little predicted secondary strucutre, was very similar to that of pSAM320 indicating that the terminal 27 nt including the internal ORF rather than extensive secondary structure may be responsible for the low basal levels of AdoMetDC expression. These results, confirmed using luciferase constructs, suggest that the negative effect on expression is predominantly due to the internal ORF. Depletion of spermine by BDAP increased the expression from pSAM320 more than 5-fold without affecting AdoMetDC mRNA levels. Expression from pSAM293 was unchanged by spermine depletion, whereas that from pSAM320-ATG was increased 2.5-fold. These results indicate the presence of a spermine response element in the first 27 nt of the 5′UTR that may include but is not entirely due to the internal ORF.

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Primary structure of rat plasma membrane Ca2+-ATPase isoform 4 and analysis of alternative splicing patterns at splice site A

Biochemical Journal ◽

10.1042/bj3060779 ◽

1995 ◽

Vol 306 (3) ◽

pp. 779-785 ◽

Cited By ~ 45

Author(s):

T P Keeton ◽

G E Shull

Keyword(s):

Plasma Membrane ◽

Alternative Splicing ◽

Splice Site ◽

Primary Structure ◽

Sequence Divergence ◽

Rat Plasma ◽

Pcr Analysis ◽

Rat Tissues ◽

Mrna Tissue Distribution ◽

Splicing Patterns

We have determined the primary structure of the rat plasma membrane Ca(2+)-ATPase isoform 4 (PMCA4), and have analysed its mRNA tissue distribution and alternative splicing patterns at splice site A. Rat PMCA4 (rPMCA4) genomic clones were isolated and used to determine the coding sequences and intron/exon organization of the 5′-end of the gene, and the remaining coding sequence was determined from PCR-amplified cDNA fragments. Pairwise comparisons reveal that the amino acid sequence of rPMCA4 has diverged substantially from those of rPMCA isoforms 1, 2 and 3 (73-76% identity) and from that of human PMCA4 (87%). Despite the high degree of sequence divergence between the two species, comparisons of intron and untranslated mRNA sequences with the corresponding human sequences confirm the identity of this rat isoform as PMCA4. Northern blot studies demonstrate that the PMCA4 mRNA is expressed in all rat tissues examined except liver, with the highest levels in uterus and stomach. A combination of PCR analysis of alternative splicing patterns and sequence analysis of the gene demonstrate that a 36 nt exon at site A is included in PMCA4 mRNAs of most tissues but is largely excluded in heart and testis. Alternative splicing of both the 36 nt exon and a previously characterized 175 nt exon at splice site C, each of which can be either included or excluded in a highly tissue-specific manner, leads to the production of four different PMCA4 variants ranging in size from 1157 to 1203 amino acids.

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