On the biotopology of protein biosynthesis

The present paper is an attempt to outline a possible approach to the study of concrete cellular systems in terms of relational biology as developed by Rashevsky and Rosen. The basic ideas and the formalism of Rosen’s (M,R)-systems, proposed as a model of abstract biological systems, are used in order to represent the cellular protein biosynthesis. A diagram corresponding to the activation of amino acids and synthesis of amino-acyl-transfer RNA, the attachment of _t RNA to a specific codon of messenger RNA and peptide bond synthesis with the release of a protein molecule, is constructed. The systemM thus obtained for the synthesis of a proteinp _k receives a set of environmental inputs, that is, the twently naturally occurring amino acids and emits a single output, thep _k protein. The problem of noncontractibility of inputs in the system is then analyzed. In our context, it is found that the noncontractibility is not associated with the whole amino acid setS _pk but with an “essential amino acid set” , so that and represent the set of amino acids which can be replaced or absent. According to our considerations, the biochemical concept of “essential amino acid” acquires a new significance, that is, what seems “essential” is linked with the ability to form a giventRNA _t ∼a _i complex in a suitable augmented dependent set essential for the biosynthesis of a functional protein. Eventually the discussion of re-establishability leads to some important biological implications concerning the existence of ambiguous codons and the degeneracy phenomenon in the genetic code, as anecessary biochemical tool involved in adaptive processes.     

The cDNA sequence and the deduced amino acid sequence of human transcobalamin II show homology with rat intrinsic factor and human transcobalamin I.

The cellular uptake of cobalamin (Cbl, vitamin B12) is mediated by transcobalamin II (TCII), a plasma protein that binds Cbl and is secreted by human umbilical vein endothelial (HUVE) cells. These cells synthesize and secrete TCII and, therefore, served as the source of the complementary DNA (cDNA) library from which the TCII cDNA was isolated. This full-length cDNA consists of 1866 nucleotides that code for a leader peptide of 18 amino acids, a secreted protein of 409 amino acids, a 5'-untranslated segment of 37 nucleotides, and a 3'-untranslated region of 548 nucleotides. A single 1.9-kilobase species of mRNA corresponding to the size of the cDNA was identified by Northern blot analysis of the RNA isolated from HUVE cells. TCII has 20% amino acid homology and greater than 50% nucleotide homology with human transcobalamin I (TCI) and with rat intrinsic factor (R-IF). TCII has no homology with the amino-terminal region of R-IF that has been reported to have significant primary as well as secondary structural homology with the nucleotide-binding domain of NAD-dependent oxidoreductases. The regions of homology that are common to all three proteins are located in seven domains of the amino acid sequence. One or more of these conserved domains is likely to be involved in Cbl binding, a function that is common to all three proteins. However, the difference in the affinity of TCII, TCI, and R-IF for Cbl and Cbl analogues indicates, a priori, that structural differences in the ligand-binding site of these proteins exist and these probably resulted from divergence of a common ancestral gene.     

Transformation of NIH 3T3 cells by enhanced PAR expression

Prostate androgen regulated (PAR) is a 1038bp novel gene located on chromosome 1 in epidermal differentiation complex. The gene is ubiquitously expressed in normal tissues and is overexpressed in most of their malignant counterparts. PAR cellular function is unknown. Here we report the effect of increased PAR expression induced by transfection of PAR cDNA on NIH3T3 cell phenotype. PAR-NIH3T3 transfectants expressing 3- to 4-fold higher PAR levels compared to controls grew faster in tissue cultures, formed colonies in soft agar, and exhibited a shortening of G1 and S phases of cell cycle and formed tumors in SCID mice. Transfection of NIH3T3 cells with increased ectopic PAR expression with a 22 mer oligonucleotide in antisense orientation with PAR mRNA abrogated their ability to form colonies in soft agar. The data presented here along with our previously reported results on DU145 cells transfected with antisense PAR cDNA suggest that PAR gene behaves like a proto-oncogene.     

Isolation of the complementary DNA for human transcobalamin II

A complementary DNA (cDNA) clone coding for transcobalamin II (TCII) has been isolated from a human umbilical vein endothelial cell cDNA library. The cDNA is 1.9 Kb and includes the nucleotide sequence which encodes the NH2-terminal 19 amino acids of human TCII. The size of the cDNA is sufficient to code for the entire protein and also contains the nucleotide sequence coding for a 24 amino acid leader peptide and a long untranslated 3' region. The availability of this cDNA will provide the opportunity to characterize genetic disorders of TCII.     

A theoretical model for the control mechanisms in biochemical reactions

A mathematical representation for the analysis of control mechanisms in biochemical reactions is presented. First, the theoretical concept of concentration in biological systems is developed. Then a system consisting of two functions λ and τ is constructed as a network of single output automata. The range of λ is taken to be formed by a set of twostates qualitatively different from the “repair function” Φ _f of a mappingf: A→B in the stimulated Φ¹ and unstimulated state Φ⁰. Likewise, the range of τ is formed by the set δ={f ^o ,f ¹} wheref ¹ means the mappingf in its stimulated state andf ^o in the unstimulated one. It is demonstrated that the mathematical structure described acts as a control mechanism over thef and Φ _f , so that two biochemical components,A→B, are transformed at a controlled rate. Some of the biological applications of this model are briefly examined. The Jacob-Monod model, the enzymatic adaptation phenomenon, and the “rheon unit” hypothesis are discussed within our framework. Eventually, a concrete model for the RNA-polymerase mechanism, based on the above discussion, is presented.