On the Species Specificity of Acceptor RNA and Attachment Enzymes

One of the steps in protein biosynthesis appears to be the attachment of each amino acid to a specific acceptor (SRNA) molecule. According to the adaptor hypothesis, each SRNA molecule would then fit to a specific complementary base sequence on a linear RNA template, specifying the sequence of amino acids in the resultant protein [1,2]. An adaptor molecule thus could have two specificities: one recognizing the correct amino acid and activating enzyme; the other, the proper position on the template. The correctness of the amino-acid sequence therefore would depend upon the precision and constancy of the adaptors. However, the structures of the enzymes and adaptors are presumably under the genetic control of the organism and might be subject to heritable modifications. It is therefore conceivable that one or both ends of an adaptor might change sufficiently to cause occasional errors and, in the long run, an alteration of the genetic code might evolve. This notion, prompted by genetic observations [3] which suggested that mutation of a bacterium might modify its translation of genetic information, lead to the present comparison of the specificities of the acceptor RNA and activating enzymes of different organisms. Several differences in specificity have been reported previously. Berg et al. [4] demonstrated that SRNA from Escherichia coli contains two distinguishable acceptors for methionine. An enzyme prepared from yeast could attach methionine to one of these, while the enzyme from E. coli could attach to both. Webster found, in pig liver, a difference between the nuclear and cytoplasmic attachment enzymes for alanine. Rendi and Ochoa [6] noted that, for leucine, the enzymes in yeast and in E. coli could attach only to their homologous SRNA. Furthermore, in the case of leucine, rat liver enzyme and SRNA were interchangeable with those from E. coli. The observations presented below show that whether the enzymes and/or acceptors from two organisms are interchangeable depends upon not only the organisms in question but also the particular amino aci

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective.

Hemagglutinins (HA's) from duck, swine, and human influenza viruses have previously been shown to prefer avian and human glycan receptor analogues with distinct topological profiles, pentasaccharides LSTa (alpha-2,3 linkage) and LSTc (alpha-2,6 linkage), in comparative molecular dynamics studies. On the basis of detailed analyses of the dynamic motions of the receptor binding domains (RBDs) and interaction energy profiles with individual glycan residues, we have identified approximately 30 residue positions in the RBD that present distinct profiles with the receptor analogues. Glycan binding constrained the conformational space sampling by the HA. Electrostatic steering appeared to play a key role in glycan binding specificity. The complex dynamic behaviors of the major SSE and trimeric interfaces with or without bound glycans suggested that networks of interactions might account for species specificity in these low affinity and high avidity (multivalent) interactions between different HA and glycans. Contact frequency, energetic decomposition, and H-bond analyses revealed species-specific differences in HA-glycan interaction profiles, not readily discernible from crystal structures alone. Interaction energy profiles indicated that mutation events at the set of residues such as 145, 156, 158, and 222 would favor human or avian receptor analogues, often through interactions with distal asialo-residues. These results correlate well with existing experimental evidence, and suggest new opportunities for simulation-based vaccine and drug development

Species- and organ-specificity of secretory proteins derived from human prostate and seminal vesicles

Polyclonal antibodies against semenogelin (SG) isolated from human seminal vesicle secretion and acid phosphatase (PAP), β‐microseminoprotein (β‐MSP), and Prostate‐Specific Antigen (PSA) derived from human prostatic fluid, as well as a monoclonal antibody against β‐MSP were used for immunocytochemical detection of the respective antigens in different organs from different species. SG immunoreactivity was detected in the epithelium of the pubertal and adult human and in monkey seminal vesicle, ampulla of the vas deferens, and ejaculatory duct. PAP, β‐MSP, and PSA immunoreactivities were detected in the pubertal and adult human prostate and the cranial and caudal monkey prostate. With the exception of a weak PSA immunoreactivity in the proximal portions of the ejaculatory duct, none of the latter antisera reacted with seminal vesicle, ampullary, and ejaculatory duct epithelium. Among the non‐primate species studied (dog, bull, rat, guinea pig) only the canine prostatic epithelium displayed a definite immunoreactivity with the PAP antibody and a moderate reaction with the PSA antibody. No immunoreaction was seen in bull and rat seminal vesicle and canine ampulla of the vas deferens with the SG antibody. The same was true for the (ventral) prostate of rat, bull, and dog for β‐MSP. The epithelium of the rat dorsal prostate showed a slight cross‐reactivity with the monoclonal antibody against β‐MSP and one polyclonal antibody against PSA. The findings indicate a rather strict species‐dependent expression of human seminal proteins which show some similarities in primates, but only marginal relationship to species with different physiology of seminal fluid

Species Specificity in Major Urinary Proteins by Parallel Evolution

Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1) diversity, to enable the signaling of multiple behaviors, 2) dynamic regulation, to indicate age and dominance, and 3) species-specificity. Recently, the major urinary proteins (Mups) have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues

Experimental studies of species-specificity in cecropia-ant relationships

Journal ArticleStrict coevolution requires that interactions among organisms be speciesspecific. We assessed the relative roles of host- and habitat-specificity in determining the match between a genus of myrmecophytic trees and a guild of obligate plant-ants in the moist tropical forests of Madre de Dios, Peru. Four locally coexisting but habitat-restricted Cecropia species were cultivated in screen tents until all plants had developed myrmecophytic traits. Saplings were then placed within replicate blocks of each of two habitat types: riversides and small forest light gaps. Colonization events were recorded every 3 d between June and August of 1992, and queens were later removed from stem internodes for identification and brood censuses. A similar experiment, conducted in September through November of 1993, included just two species of Cecropia hosts. Effects of host species and habitat on queen colonization rates were evaluated by log-likelihood goodness-of-fit tests and contingency table tests. For three ant species, we also conducted queen preference experiments to compare queen behaviors across a range of host plants. Differences among ants in the extent of habitat-specificity vs. host-specificity provide evidence for multiple evolutionary routes to obligate association with Cecropia. Habitat- specificity exceeded host-specificity in Azteca ovaticeps (Dolichoderinae), for which queen preference experiments revealed no significant discrimination among hosts. This extreme riverside specialist is thought to have descended from generalist live-stem nesters in secondgrowth habitats. In Azteca australis, host-specificity was strong, and in this species only, directed toward hosts where brood production was most successful. Conflicting habitat associations in the two experiments indicated the weakness or absence of a consistent habitat affiliation in Azteca australis and suggested that colonization frequencies were influenced instead by proximity to foundress sources. Close relatives of A. australis live in exposed carton nests, which may have been positioned ancestrally on key resource plants, e.g., those producing lipid- and amino-acid-rich pearl bodies. Pachycondyla luteola (Ponerinae) exhibited both strong habitat and host associations and may have undergone pairwise coevolution with its forest-gap-dwelling primary host. Queens of Camponotus balzani (Formicinae), possibly a recent and secondary associate of Cecropia, were overrepresented in forest gap habitat but were host generalists, underrepresented only on a host with extremely small internodes. Apparently greater host-specificity in C. balzani at later stages of colony establishment may be due to differential post colonization mortality on the various hosts. Attack of ant queens by parasitoid wasps was strongly concentrated in the linear riverside habitat and weak to absent in the patchily distributed forest gap habitat. Due to lower rates of either parasitoid attack or other forms of queen mortality, Camponotus balzani experienced greater success in the forest gap habitat, where it was overrepresented in colonization experiments. Historical coincidences and preadaptations appear to have strongly influenced pairings between Cecropia species and their obligate plant-ants and account for much of the "apparent" niche partitioning observed in the system. Species-specificity seems to be determined mainly by coincident habitat affiliations of ants and plants ("coordinated dispersal") and by preadapted capacities of ants to distinguish among host-plant species. Multiple mechanisms for species-specificity may be characteristic of relationships in which associates disperse separately from one another (i.e., show horizontal transmission). Our results are consistent with the view that coadaptation and co-cladogenesis are more likely in systems where dispersal of associates is tightly coupled

Mating pair stabilization mediates species specificity during bacterial conjugation

Bacterial conjugation is a contact-dependent form of horizontal gene transfer where DNA is transferred in a unidirectional manner from a donor to recipient bacterium. It is also a key driver of the spread of antimicrobial resistance plasmids within clinically important pathogens. The intimate attachment of cells within a conjugating pair is crucial for efficient DNA transfer. However, the mechanism underlying the formation of tight mating junctions, which occurs through a process termed mating pair stabilization (MPS), is unclear. This work describes how variants of the plasmid-encoded outer membrane protein TraN interact with different receptors on recipient cells to mediate MPS. Using a reporter plasmid generated from the Klebsiella pneumoniae carbapenem resistance plasmid pKpQIL, mutations in the major outer membrane porin OmpK36 were found to reduce plasmid uptake in recipients. Meanwhile, substitution of traN on this plasmid with traN from two related plasmids, the Shigella flexneri resistance plasmid, R100-1 and the prototypical F plasmid, revealed that these TraN variants mediate dependency on recipient OmpW and OmpA respectively instead. Structural analysis showed that TraN from pKpQIL forms a complex with OmpK36 via the insertion of a β-hairpin structure into one of the subunits of the trimeric porin. Combining bioinformatic analysis and structural predictions using AlphaFold, four additional TraN variants were identified. All seven TraN variants could be classified into four groups based on their structural similarity and associated receptors: TraNα (OmpW), TraNβ (OmpK36), TraNγ (OmpA) and TraNδ (OmpF). Species specificity was also observed during MPS as not all homologues of a receptor are recognized by each TraN. This specificity was reflected in the real-world host distribution of conjugative IncF plasmids suggesting that MPS plays an influential role in shaping the host range of these plasmids. These findings provide a precedent for developing strategies that target MPS to mitigate resistance gene dissemination.Open Acces

Species Authentication of Dog, Cat, and Tiger Using Cytochrome Β Gene

Adulteration of animal food products for economic reason has happened during the last decades. Species identification method development was needed to prevent falsification information. The objective of this research was to study species authentication (dog, cat, and tiger) to ensure animal origin in products using cyt β gene specific marker. DNA extraction and fragment amplification were conducted using phenol-chloroform and multiplex PCR (Polymerase Chain Reaction) method, respectively. This research showed that fragment length of amplification for species tested (dog, cat, and tiger) were 523, 331, 319 bp, respectively. Species specificity was also indicated by high reverse primers homology percentage. Multiplex PCR technique succeed to amplify DNA fragment from species tested, but has a limitation to amplify total DNA composite of mix DNA

V3 Tip-Dependent Species Specificity of HIV-1 Env

Molecular interactions of the variable envelope gp120 subunit of HIV-1 with two cellular receptors are the first step of viral infection, thereby playing pivotal roles in determining viral infectivity and cell tropism. However, the underlying regulatory mechanisms for interactions under gp120 spontaneous variations largely remain unknown. Here, we show an allosteric mechanism in which a single gp120 mutation remotely controls the ternary interactions between gp120 and its receptors for the switch of viral cell tropism. Virological analyses showed that a G310R substitution at the tip of the gp120 V3 loop selectively abolished the viral replication ability in human cells, despite evoking enhancement of viral replication in macaque cells. Molecular dynamics (MD) simulations predicted that the G310R substitution at a site away from the CD4 interaction site selectively impeded the binding ability of gp120 to human CD4. Consistently, virions with the G310R substitution exhibited a reduced binding ability to human lymphocyte cells. Furthermore, the G310R substitution influenced the gp120-CCR5 interaction in a CCR5-type dependent manner as assessed by MD simulations and an infectivity assay using exogenously expressed CCR5s. Interestingly, an I198M mutation in human CCR5 restored the infectivity of the G310R virus in human cells. Finally, MD simulation predicted amino acid interplays that physically connect the V3 loop and gp120 elements for the CD4 and CCR5 interactions. Collectively, these results suggest that the V3 loop tip is a cis-allosteric regulator that remotely controls intra- and intermolecular interactions of HIV-1 gp120 for balancing ternary interactions with CD4 and CCR5

Latent regulatory potential of human-specific repetitive elements

At least half of the human genome is derived from repetitive elements, which are often lineage specific and silenced by a variety of genetic and epigenetic mechanisms. Using a transchromosomic mouse strain that transmits an almost complete single copy of human chromosome 21 via the female germline, we show that a heterologous regulatory environment can transcriptionally activate transposon-derived human regulatory regions. In the mouse nucleus, hundreds of locations on human chromosome 21 newly associate with activating histone modifications in both somatic and germline tissues, and influence the gene expression of nearby transcripts. These regions are enriched with primate and human lineage-specific transposable elements, and their activation corresponds to changes in DNA methylation at CpG dinucleotides. This study reveals the latent regulatory potential of the repetitive human genome and illustrates the species specificity of mechanisms that control it