Understanding the Genetic Code

The genetic code is the sequence of nucleotide bases in nucleic acids (DNA and RNA) that code for amino acid chains in proteins. DNA consists of the four nucleotide bases: adenine (A), guanine (G), cytosine (C) and thymine (T). RNA contains the nucleotides adenine, guanine, cytosine and uracil (U). When three continuous nucleotide bases code for an amino acid or signal the beginning or end of protein synthesis, the set is known as a codon. These triplet sets provide the instructions for the production of amino acids. Amino acids are linked together to form proteins.

Breaking the second genetic code

Diverse messenger RNAs, and thus proteins, can be generated from a single piece of DNA. A computational approach is helping to uncover complex combinatorial rules by which specific gene instructions are selected.

At face value, it all sounds simple: DNA makes RNA, which then makes protein. But the reality is much more complex. For instance, depending on what further processing the transcribed messenger RNA sequence undergoes before being translated into a protein, it could code for different proteins.

Tailoring of Membrane Proteins by Alternative Splicing of Pre-mRNA

In 1941, Beadle and Tatum provided data that led to the “one gene, one protein” paradigm (). This paradigm persisted until researchers began to explore the human genome in depth, at which point it was discovered that the number of protein-encoding genes is much lower than originally predicted—leading to the “one gene, many proteins” hypothesis. Seminal work with adenovirus (, ) first led to the notion that multiple transcripts can arise from the same precursor RNA molecule. In 1978 a new mechanism, now known as alternative splicing (AS), was proposed () to generate proteomic diversity from a single gene in eukaryotes, and experimental confirmation quickly followed ().

Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes

Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions.

It is well acknowledged that phenotypic and functional diversity are contributed by the variable transcription of genes in eukaryotes to a considerable extent []. The genic transcription could vary in terms of mRNA molecules and expression levels. In the case of the former, the same gene could be alternatively transcripted into more than one of the mRNA molecules with similar but not identical functions, and this one-to-several relationship of gene to mRNAs mainly results from alternative splicing of pre-mRNA [].

RNA processing errors triggered by cadmium and integrator complex disruption are signals for environmental stress

For most eukaryotic genes, introns must be spliced out of precursor mRNA (pre-mRNA) to produce mature mRNA transcripts ready for translation [], a process that is essential to organismal development and homeostasis [, ]. Splicing is predominantly conducted in the nucleus by the spliceosome and associated RNA-binding proteins that form a dynamic, extremely complicated, and poorly understood macromolecular complex of small nuclear RNAs (snRNAs) and up to 300 distinct proteins []. In the last decade, an additional metazoan-specific complex of at least 14 proteins, named integrator, was discovered that indirectly promotes splicing by processing snRNAs into their functional forms [–].

Responses to environmental stress almost always include transcriptional activation of genes encoding proteins that mitigate damage. However, translation of these stress response genes can be delayed if they contain introns and splicing is disrupted. In eukaryotes of all kingdoms, genes that are rapidly induced during stress contain few introns as a strategy to bypass splicing []. Genes encoding canonical heat shock protein (HSP) chaperone genes exemplify this strategy []. Coincidentally, HSPs have been shown to help restore RNA splicing during stress, presumably by promoting proper folding of splicing factor proteins [, –]. Other stress-responsive and intronless genes are poorly studied.

Classes of non-conventional tetraspanins defined by alternative splicing

Tetraspanins emerge as a family of membrane proteins mediating an exceptional broad diversity of functions. The naming refers to their four transmembrane segments, which define the tetraspanins‘ typical membrane topology.

Besides isoforms with four transmembrane segments, most mRNA sequences are coding for isoforms with one, two or three transmembrane segments, representing structurally mono-, di- and trispanins. Moreover, alternative splicing may alter transmembrane topology, delete parts of the large extracellular loop, or generate alternative N- or C-termini.

The increase in gene products by alternative splicing is associated with an unexpected high structural variability of tetraspanins.

non-conventional tetraspanins have roles in regulating ER exit and modulating tetraspanin-enriched microdomain function.