Journal of Molecular Evolution

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either α-helical or β-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the downstream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Computational and experimental attempts tried to characterize a universial core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiments suggest a much larger set of essential genes (certainly more than several hundreds, even under the most restrictive hypotheses) that is dependent on the biological complexity and environmental specificity of the organism. Highly biased genes, which are generally also the most expressed in translationally biased organisms, tend to be over represented in the class of genes deemed to be essential for any given bacterial species. This association is far from perfect; nevertheless, it allows us to propose a new computational method to detect, to a certain extent, ubiquitous genes, nonorthologous genes, environment-specific genes, genes involved in the stress response, and genes with no identified function but highly likely to be essential for the cell. Most of these groups of genes cannot be identified with previously attempted computational and experimental approaches. The large variety of life-styles and the unusually detectable functional signals characterizing translationally biased organisms suggest using them as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds.

In recent years a wide variety of biochemical and molecular typing systems has been employed in the study of parasite diversity aimed at investigating the level of genetic diversity and delineating the relationship between differcnt species and subspecies. However, such methods have failed to differentiate between two of the classically defined subspecies of the protozoan parasite Trypanosoma brucei: the human infective, T. b. rhodesiense, which causes African sleeping sickness, and the non-human infective T. b. brucei. This has led to the hypothesis that T. b. rhodesiense is a host range variant of T. b. brucei. In this paper we test this hypothesis by examining highly polymorphic tandemly repeated regions of the trypanosome genome, i.e., minisatellite loci. We have employed the technique of minisatellite variant repeat mapping by PCR (MVR-PCR), which determines the distribution of variant repeat units along the tandem array of one minisatellite, MS42. The maps generated by this technique not only allow unequivocal allele identification but also contain within them cladistic information which we used to determine the possible genetic relationship between the different subspecies of T. brucei. Our findings revealed that human infective (T. b. rhodesiense) isolates from Uganda are more closely related to the local non-human infective isolates (T. b. brucei) than they are to other human infective stocks from different regions, suggesting that human infectivity has originated independently in these different geographical regions. This would infer that the separate classification of all human infective stocks from East Africa into the subspecies T. b. rhodesiense is genetically inappropriate and it would be better to consider geographically separate populations as host range variants of T. brucei brucei or perhaps as a series of different subspecies. Based on these data, it is clear that MVR mapping is a very useful tool for the analysis of zoonotic eukaryotic pathogens where delineation of the origins of outbreaks of disease and definition of human infective strains are key questions.

Deoxyribozymes that could catalyze the formation of an internucleotide phosphorothioester linkage were selected from a random sequence pool. During the course of the selection, the pool was successively challenged with five oligonucleotide substrates, each of which terminated in the same hexanucleotide sequence. Selected deoxyribozyme ligases could use all five substrates, albeit to different degrees, and appeared to form secondary structures that allow differential pairing between the deoxyribozyme and each substrate. These results suggest that early replicases may have been able to bind a variety of oligonucleotide substrates while catalyzing ligation via a common junction.

Các nghiên cứu tiến hóa trong các hiệp hội địa y theo chân sinh vật cộng sinh nấm (mycobiont), là sinh vật cộng sinh mà địa y được đặt tên và chiếm phần lớn thallus. Tuy nhiên, sự tiến hóa của đối tác tảo (photobiont) cũng rất quan trọng để duy trì tính tương thích giữa các sinh vật cộng sinh và tối ưu hóa năng suất của hiệp hội địa y. Các vùng spacer nội bộ (ITS) của DNA ribosome hạt nhân (rDNA) đã được nghiên cứu để xác định các mẫu trình tự DNA chính và các mẫu trong cấu trúc thứ cấp của các trình tự rRNA ở cả hai sinh vật cộng sinh thuộc giống Cladonia. Các sinh vật cộng sinh nấm và tảo cho thấy những xu hướng trái ngược về tốc độ tiến hóa và chiều dài đoạn. Cả hai sinh vật cộng sinh đều cho thấy sự bảo tồn mạnh mẽ hơn của cấu trúc ITS2 so với cấu trúc ITS1. Sự tương đồng là rõ ràng trong các cấu trúc thứ cấp giữa hai nhóm thuỷ sinh chi diệp và nấm ascomycete khác nhau. Hầu hết các loài nấm và tất cả các phức hợp loài đều phi đa nguồn gốc. ITS rDNA của tảo địa y tự nhiên từ Manitoba và bốn loài tảo đã biết có độ tương đồng cao. Tảo địa y tự nhiên phân tách thành các nhánh được hỗ trợ mạnh bởi các đặc điểm môi trường, cho thấy rằng tảo đã thích nghi với môi trường có thể kết hợp với các hạt giống nấm đang nảy mầm thuộc giống Cladonia. Tính linh hoạt của nấm có thể cho phép mycobiont thích nghi với môi trường của photobiont, tạo ra sự biến đổi trong hình thái địa y. Điều này có thể giải thích sự không tương đồng của các mẫu phát sinh chủng loại giữa các đối tác tảo và nấm đã được thử nghiệm và sự đa nguồn gốc của các loài nấm.

Extensive knowledge exists inEscherichia coli about the contiguouspheA andaroF-tyrA operons which have opposite transcription orientations and are separated by a bidirectional transcription terminator. The corresponding structural genes and individual components of the terminator and attenuator fromErwinia herbicola have been analyzed from an evolutionary vantage point. A 7.5-kb DNA fragment fromE. herbicola carrying the linkedpheA, tyrA, andaroF genes was cloned by functional complementation ofE. coli auxotrophic requirements. A 3,433-bp segment of DNA consisting of more than half ofaroF, all oftyrA, and the entire phenylalanine operon (promoter, leader region encoding the leader peptide and containing thephe attenuator, andpheA) was sequenced. A bidirectional transcription terminator was positioned between the divergently transcribedpheA andtyrA. The adjacentaroF andtyrA genes share a common transcription orientation, consistent with their probable coexistence within an operon. However,tyrA can be expressed efficiently from an internal promoter which appears to lie within the 3′ portion ofaroF. The gene order ispheA tyrA aroF inE. herbicola, with the same tail-to-tail arrangement of transcription known to exist inE. coli. ThepheL coding region of the phe operon was dominated by phenylalanine codons, seven of the 15 amino acid residues of the leader peptide beingl-phenylalanine. TheE. herbicola pheA andtyrA genes were 1,161 by and 1,119 by in length, respectively, and corresponded to deduced gene products having subunit molecular weights of 43,182 and 41,847. The deduced amino acid sequences ofPheA andTyrA were homologous at their N-termini, consistent with a common evolutionary origin of the chorismate mutase domains present at the amino terminus of bothPheA andTyrA. A detailed comparison of theE. coli andE. herbicola sequences was made. ThepheA, tyrA, andaroF genes ofE. herbicola exhibited high overall identity with the counterpartE. coli genes. Within the leader region of thephe operon, the leader peptide coding region was highly conserved. Although the 1:2 and 2′:3′ stems defining the pause structure and the antiterminator, respectively, were also highly conserved, RNA segment 4 of the attenuator terminator exhibited considerable divergence, as did the distal portion of the attenuator region. Within the span of attenuator region encoding the three stern-loop structures of mRNA secondary configuration, hot spots of base-residue divergence were localized to looped-out regions. No changes occurred which would simultaneously disrupt alternative pairing relationships of secondary configuration. The bidirectional terminator betweenpheA andtyrA has diverged very substantially. Much of the promoter region and the untranslated region between the promoter and thepheL coding region also differed considerably between the two organisms.

Sulphur may have played an important role, mainly as an energy converter, during the initial steps of Chemical Evolution. In atmospheric processes, sulphur, in the form of H2S might have been a primary energy acceptor and a source of hot hydrogen atoms. The presence of H2S in the primeval earth atmosphere with a molar ratio of about 10−2 could have allowed the formation of several volatile S-containing compounds without inhibiting the synthesis of the reactive products which are formed in the absence of H2S. An evaluation of the quantity of H2S which could have been included in the primeval atmosphere suggests that such a molar ratio may have been reached. In the primitive soup, the thiols and sulphides formed in the gaseous phase may have evolved, giving rise to various prebiotic syntheses. Studies on the addition reaction of alkanethiols on malonic nitriles in aqueous solutions show two different condensation processes: the formation of thioethers and the formation of iminothioesters. Taking into account the values of the specific rate constants for the two reactions, it is shown that these reactions may have taken place in the primitive earth conditions. These two compounds may have played an important role in the prebiochemical evolution. In particular, iminothioesters can be considered as the immediate precursors of thioesters.