An unpublished paper on genes without introns

The following paper was part of the case I made in the 1990s that introns reflected the pressure for stem-loop potential in genomes. Difficulties getting other papers in the series (see elsewhere in these web-pages) accepted for publication, led to this one (drafted in 1995 and last accessed and saved in 1998) never being submitted for publication. However, a decade later Jeffares, Penkett & Bahler (2008 Trends in Genetics 24, 375-378) reported "that genes with rapidly changing expression levels in response to stress contain significantly lower intron densities" and proposed that introns were "selected against in genes whose transcripts require rapid adjustment for survival of environmental challenges." Although they invoked many good reasons why this might be so, the stem-loop secondary structure of nucleic acids was not mentioned. Accordingly, this paper was unearthed, dusted off, and placed here (with minimal further editing; e.g. removal of some superfluous references). A more exhaustive examination of heat-shock genes would seem necessary before formal submission to a journal.

ADDED NOTE July 2015: FORS-D analysis of nucleic acid structure has now been supplemented by other approaches that have been applied to multiple sequences. In plant seedlings (Arabidopsis thaliana) it is found that "mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide [i.e. less cohesive structure]" (Ding et al. 2014. Nature 505, 696-700). Thus, they discovered that "genome-wide relationships exist between in vivo mRNA structures and biological functions of the encoded proteins." They suggest that "stress-response RNAs may be more plastic, changing their structure in response to changing cellular conditions." Indeed, the positive FORS-D values reported below, indicate that base order has evolved to actively prevent the formation of higher ordered structure.

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Negative base order-dependent stem-loop potential of heat shock protein 70 genes indicates evolutionary selection to avoid mRNA secondary structure

D. R. Forsdyke [ draft unsubmitted paper]

Keywords: recombination, stem-loop, homology search, introns, heat-shock protein, (G+C)/(A+T) ratio, speciation.

Abbreviations: FONS = folding of natural seqence; FORS-M = folding of randomized sequence mean; FORS-D = folding of randomized sequence difference.

Running head: Stem-loop Model for Initiation of Recombination

There has been an evolutionary selection pressure on base order favouring the distribution of stem-loop potential throughout genomes. If this pressure can be accommodated by the use of synonymous codons and conservative amino acid exchanges, then long coding regions are possible. Failing this, proteins are encoded in segments of low stem-loop potential (exons) interrupted by regions of high stem-loop potential (introns). This is particularly evident in genes under strong positive Darwinian selection. The intronless heat shock protein 70 gene turns out to be a special case. Being highly conserved (i.e. under negative evolutionary selection pressure), and with one of the longest know open reading frames, high stem-loop potential would be expected. However, the opposite is found. It is suggested that heat shock protein 70 proteins must be synthesized rapidly in response to intracellular stresses. This requires rapid transcription under circumstances which might impair RNA splicing, and minimization of RNA secondary structure to permit rapid translation. The potential to form stem-loops appears to have been decreased by these needs.

Introduction

Heat-shock 70 proteins are synthesized rapidly in response to various biological, chemical or physically stresses, such as viral infection, ethanol and heat-shock. The genes are present in all cellular organisms and the sequences are highly conserved. A role in intracellular self/not-self discrimination has been suggested.

Heat-Shock Protein 70 as a Special Case

Among intronless genes are those encoding the heat shock proteins 70, which are very highly conserved between species. The single open reading frame of a human gene (HUMHSP70D) encodes a protein of 641 amino acids, corresponding to a sequence of 1923 nt. This is one of the longest uninterrupted open-reading frames known (Hawkins, 1988). Heat shock proteins usually need to be synthesized rapidly in response to various intracellular stresses (Forsdyke, 1994), and the absence of introns in the corresponding gene implies a need to minimize delay in transcript processing (which might itself be impaired by the heat-shock; Yost and Lindquist, 1986). The evolution of the sequence could have served this need.

FIG. 1. Fold energy minimization values (FORS-M, FONS) and differences (FORS-D) for the 2691 nt sequence corresponding to a human heat shock protein 70 gene, HUMHSP70D. There are 51 windows of 200 nt, beginning at 50 nt intervals (thus each overlaps its preceding neighbour by 150 nt). The beginning of the mRNA corresponds to a window from nt 274 to nt 473. The last window spans nt 2474-2673. The grey box indicates the exon. Vertical dashed lines in the lower figure indicate, from left to right, the beginning of the exon, the beginning of the protein-encoding region, the end of the protein coding region, and the end the exon. [Original plot prepared 27-3-1994 from file HUMHSP70D contributed to GenBank 31-7-1992 by Hunt & Morimoto (1985) Proc. Natl. Acad. Sci. USA 82, 6455.]

Figure 1 shows that, in contrast to many long open reading frame-containing genes [shown in other papers], positive FORS-D values predominate in HUMHSP70D. The average for the 39 datapoints corresponding to the coding region is 1.69sd0.62 kcal/mol. Two other heat-shock protein 70 genes gave similar results. Thus, a human gene located in the major histocompatibility complex (HUMMHHSP) has an average FORS-D value in the coding region of 1.33sd0.57 kcal/mol. A mouse homolog (MUSHP7A2) has an average FORS-D value in the coding region of 0.42sd0.91 kcal/mol. That this is not a general characteristic of single exon genes was suggested by examining two histone genes. The average FORS-D value in the coding region of a histone 3 gene (HUMHISPRM) is -5.30sd1.16 kcal/mol (9 datapoints). The corresponding value for a histone 4 gene (HUMHIS4) is -2.08sd1.59 kcal/mol (6 datapoints).

Thus, heat shock protein 70 genes would seem to be special cases. An evolutionary pressure for positive FORS-D values may have been countermanded by the need for rapid synthesis of a precise protein structure for which there are not appropriate redundant codons. Consistent with this, codon preference analysis (Gribskov and Devereux, 1991) shows minimal usage of rare human codons in HUMHSP70D (data not shown). Under heat shock conditions the use of codons corresponding to abundant tRNAs might facilitate protein synthesis. Similarly, ribosomes might transverse most rapidly mRNAs transcribed from genes which had evolved to decrease DNA (and hence RNA) secondary structure.

Acknowledgements

This work was supported by a grant from the Medical Research Council of Canada.

LITERATURE CITED

FORSDYKE, D. R. 1994. The heat shock response and the molecular basis of genetic dominance. J. Theor. Biol. 167:1-5.

FORSDYKE, D. R. 1995a. Fine-tuning of intracellular protein concentrations, a collective protein function involved in aneuploid lethality, sex-determination and speciation? J. Theor. Biol. 172:335-345.

FORSDYKE, D. R. 1995b. Relative roles of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J. Mol. Evol. (submitted)

FORSDYKE, D. R. 1995c. Selective pressures on DNA generate antisense phenomena as by-products. J. Mol. Evol. (submitted)

FORSDYKE, D. R. 1995d. Different biological species "broadcast" their DNAs at different (G+C)% "wavelengths". J. Theor. Biol. (submitted)

FORSDYKE, D. R. 1995e. Conservation of stem-loop potential in introns of snake venom phospholipase A₂ genes. An application of FORS-D analysis. Mol. Biol. Evol. (submitted)

FORSDYKE, D. R. 1995f. Paradoxical relationship between stem-loop potential and substitution density indicates that retroviral quasispecies conserve recombination function more than protein function. J. Mol. Biol. (submitted)

GRIBSKOV, M., and J. DEVEREUX. 1991. Sequence analysis primer. Stockton Press, New York.

HAWKINS, J. D. 1988. A survey of intron and exon lengths. Nucleic Acids Res. 16:9893-9905.