A reading frame is a way of dividing a nucleotide sequence into consecutive, non-overlapping groups of three, called codons. During translation, these groups determine how the information in messenger RNA is interpreted to produce a protein. Because codons contain three nucleotides, a sequence read in a given direction has three possible reading frames, depending on which nucleotide begins the first group. A reading frame specifies the grouping of bases; it does not, by itself, establish that the sequence is translated. (ncbi.nlm.nih.gov)
Three frames and six-frame analysis
Translation proceeds along RNA in the 5′-to-3′ direction. Moving the starting position by one or two nucleotides changes the codon boundaries and therefore changes the interpretation of the sequence. The following illustrative RNA sequence can be grouped in three ways:
Sequence: 5′-AUGAAACCUUGA-3′
Frame 1: AUG | AAA | CCU | UGA
Frame 2: UGA | AAC | CUU | GA
Frame 3: GAA | ACC | UUG | A
The incomplete groups at the right-hand end are not complete codons. The example demonstrates alternative groupings, not three necessarily occurring translation events. (ncbi.nlm.nih.gov)
For double-stranded DNA, sequence analysis can consider three frames on each strand, giving six possible reading frames. The opposite strand must be represented by its reverse complement and read in its own 5′-to-3′ direction, rather than simply reading the displayed sequence backward. Frames are commonly labelled +1, +2, and +3 on the displayed strand and −1, −2, and −3 on the reverse-complement strand. These labels describe sequence-analysis coordinates, not six proteins that must be produced. (ncbi.nlm.nih.gov)
Establishment and maintenance during translation
The ribosome establishes the biological reading frame when it initiates translation at a selected start codon, usually AUG. An initiator transfer RNA pairs with this codon, positioning the message for subsequent decoding. Initiation depends on surrounding signals and the translation machinery; the presence of an AUG somewhere in a sequence does not automatically make it a translation start site. (pmc.ncbi.nlm.nih.gov)
During elongation, the ribosome normally advances by one codon at a time. Coordinated interactions among the message, transfer RNAs, ribosomal components, and elongation factors preserve this three-nucleotide register. Maintaining the frame is distinct from correctly recognizing an individual codon: a decoding error can insert an incorrect amino acid without changing the boundaries of subsequent codons. (pubmed.ncbi.nlm.nih.gov)
Reading frames and open reading frames
An open reading frame (ORF) is a stretch within a reading frame that lacks an internal termination codon. In many gene-finding conventions, an ORF extends from a candidate initiation codon to an in-frame stop codon. Other conventions identify uninterrupted stop-to-stop stretches, including sequences for which the initiation site is unknown. The chosen genetic code and the permitted initiation codons affect which ORFs are identified. (ncbi.nlm.nih.gov)
A reading frame is therefore a grouping rule, whereas an ORF is a bounded candidate sequence within that grouping. One frame can contain several separate ORFs. An ORF is also not equivalent to a confirmed protein-coding gene: sequence-analysis programs identify potential coding segments, whose biological interpretation requires additional evidence. (ncbi.nlm.nih.gov)
Frameshift mutations
A frameshift mutation occurs when an insertion or deletion changes the length of a translated coding sequence by a number of nucleotides not divisible by three. This changes the grouping of bases downstream of the affected position. The resulting codons can specify different amino acids or introduce a termination signal, altering the protein product. (genome.gov)
An insertion or deletion of three nucleotides, or a multiple of three, preserves the downstream frame and is described as in-frame. It can nevertheless alter the protein substantially. Frame preservation concerns codon alignment, not whether a mutation is functionally harmless. (genome.gov)
A second, compensating insertion or deletion can restore the original downstream register. Even then, the sequence between the two changes may encode different amino acids, so restoration of the frame need not restore the original protein sequence. (digirepo.nlm.nih.gov)
Programmed changes of frame
Not every change of reading frame results from a DNA mutation. In programmed ribosomal frameshifting, signals in an RNA cause a proportion of translating ribosomes to enter another frame. A −1 shift moves the decoding register one nucleotide toward the RNA’s 5′ end relative to ordinary progression; a +1 shift moves it toward the 3′ end. The RNA sequence itself need not change. (pubmed.ncbi.nlm.nih.gov)
Such mechanisms occur in viruses and cellular organisms. They can generate alternative protein products and regulate their relative production. Many −1 frameshift signals combine a sequence that permits transfer-RNA realignment with a downstream RNA structure that influences ribosome movement. These regulated events are distinct from accidental failures to maintain the frame. (pmc.ncbi.nlm.nih.gov)
Historical significance and applications
Reading-frame analysis helped establish the triplet organization of the genetic code. In a paper published on December 30, 1961, Francis Crick, Leslie Barnett, Sydney Brenner, and Richard Watts-Tobin reported experiments with bacteriophage T4. Patterns of mutation and suppression supported a code read from a fixed starting point in groups of three bases: some combinations of frame-disrupting changes restored gene function even though individual changes did not. (digirepo.nlm.nih.gov)
In sequence analysis, identifying reading frames and ORFs helps locate candidate coding regions, translate nucleotide sequences into predicted proteins, and investigate possible frame-disrupting changes. Tools such as NCBI ORFfinder report candidate ORF coordinates and their translations, with results depending on parameters such as minimum length, genetic code, and initiation-codon criteria. Such predictions identify possibilities rather than proving that every reported segment is expressed as a protein. (ncbi.nlm.nih.gov)
References
- From RNA to Protein - Molecular Biology of the Cellncbi.nlm.nih.gov
- Frameshift Mutationgenome.gov
- ORFfinder Home - NCBIncbi.nlm.nih.gov
- Programmed translational frameshiftingpubmed.ncbi.nlm.nih.gov
- Mechanisms and implications of programmed translational frameshiftingpmc.ncbi.nlm.nih.gov
- Mechanisms and biomedical implications of –1 programmed ribosome frameshifting on viral and bacterial mRNAspmc.ncbi.nlm.nih.gov
- General Nature of the Genetic Code for Proteinsdigirepo.nlm.nih.gov