Enhanced graphic matrix analysis of nucleic acid and protein sequences.

Abstract

GeneticsEnhanced graphic matrix analysis of nucleic acid and protein sequences (sequence homology/transposition/secondary structure/immunoglobulin/microcomputer) JACOB V. MAIZEL, JR., AND ABSTRACT The enhanced graphic matrix procedure analyzes nucleic acid and amino acid sequences for features ofpossible biological interest and reveals the spatial patterns ofsuch features. When a sequence is compared to itselfthe technique shows regions of self-complementarity, direct repeats, and palindromic subsequences. Comparison of two different sequences, exemplified by immunoglobulin K light chain genes, by using colored graphic matrices showed domains of similarity, regions of divergence, and features explainable by transpositions. Analysis of mouse constant domain immunoglobulin sequences revealed self-complementary regions that can be used to fold the molecule into a structure consistent with electron microscopic observations. Computer translation of nucleic acid sequences into all possible amino acid sequences followed by graphic matrix analysis provides a way to detect theimost likely protein encoding regions and can predict the correct reading frames in sequences in which splicing patterns are not defined. Application ofthis technique to regions ofsimian virus 40 and polyoma virus demonstrates the frames of translation and shows the agreement of sequences determined in separate laboratories with different virus isolates. The graphic matrix technique can also be used to assemble fragmentary sequences during determination, to display local variations in base composition, to detect distant evolutionary relationships, and to display intragenic variation in rates of evolution.

The evolutionarily conserved region of the U snRNA export mediator PHAX is a novel RNA-binding domain that is essential for U snRNA export

“…In this study, we have performed a systematic analysis of PHAX, and revealed three important interaction domains within the protein that are all required for U snRNA export+ First, we have mapped NLSs of PHAX that are required for recycling of PHAX to the nucleus+ Second, we have found that the evolutionarily conserved region of PHAX is a novel RNA-binding domain required for mediating U snRNA export+ Third, the interaction domain of PHAX with CBC was shown to be at least partly distinct from the NLSs and the RNA-binding domain+ Our previous work had shown that the NEScontaining region of PHAX, together with PHAX phosphorylation, is required for interaction between PHAX and CRM1/Exportin1 (Ohno et al+, 2000)+ Thus, mutant forms of PHAX that allow the effects of its various in- (Maizel & Lenk, 1981) from the Wisconsin Package, version 10+1, Genetics Computer Group (GCG), with the settings of stringency 13 and window 35+ B: Sequence alignment of mouse PHAX (amino-acid residues 215-327) with the corresponding regions from rat (X67877), human (AW607076), newt (CAB54141), X. laevis (AW147615, AW148211), Drosophila melanogaster (AAF58985), C. elegans (AAF36030) and Arabidopsis thaliana (BAB02826)+ Sequences were compiled and analyzed using BLAST (Altschul et al+, 1997) and Clustal_X (Thompson et al+, 1998), and displayed using the BOXSHADE 3+21 program (http://www+ch+embnet+org/software/BOX_form+html)+ The residues indicated by closed circles in the mouse sequence were replaced by alanines in the CM1-7 mutants+ C: Poly U Sepharose binding assay with the alanine mutants+ The experiment was performed as in Figure 4+ D: Quantitation of RNA-binding activity of the alanine mutants from three experiments similar to C+ teractions on function in U snRNA export to be tested have now been generated and analyzed+…”

Evolution of Tandemly Repeated Sequences: What Happens at the End of an Array?

“…Once sequences were obtained, manipulations were performed using ESEE (Cabot and Beckenbach 1989). Dot-plot comparisons were performed using the algorithm of Maizel andLenk (1981) available in GCG (Genetics Computer Group, Madison, WI, Version 8.0, 1994).…”

“…Another alternative to nonhomologous recombination is that the PSR2 repeat family evolved from NATE. To determine if there were large-scale similarities between the PSR2 sequence and the region of NATE underlying the junction, dot-plot comparisons (Maizel and Lenk 1981) were performed. A 229-bp region of NATE P5 leading up to the junction site, the four PSR2 repeats, and 100 bp of NATE P16 on the other side of the junction site were joined into a composite sequence and this was compared to the PSR2-1 sequence.…”

Mechanism and regulation of Mg-chelatase

“…Proline residues are thought to be important in protein-protein interactions [40] and this region may be important in interacting with the H or I subunits. Figure 3 shows a Dot-plot comparison [41] of the subunit I consensus sequence shown in Figure 1 with a subunit D consensus generated from the three D subunit sequences. Diagonal lines on this Figure show regions of similarity between the two compared sequences, and it is obvious that the N-terminal of the D subunits show similarity to the I subunit.…”