Plant histones. Relevance to the evolution of prokaryotes to eukaryotes

There are many procaryotic and eucaryotic organisms in plant kingdom. It is hoped that the study of plant histones will be useful in evolutionary studies. The histones of great variety of animal species have been studied and well characterized. Less information is available concerning plant histones. The general conclusion drawn from these investigations is that most organisms of eucaryotic plant and animal species contain the same five major histone fractions. Recently the histone-like proteins were found in some primitive eucaryotes and procaryotes. Data on histones from higher and lower eucaryotes and histone-like proteins of procaryotes are reviewed. Evolution of histones and their appearance prior to that of eucaryotic cell is postulated. The role of histones in evolution of nucleosomes is discussed.     

Genomic analyses and the origin of the eukaryotes

The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the 'tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or 'ring' rather than a 'tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes.     

低等白蚁肠道共生微生物的多样性及其功能

低等白蚁肠道里存在着复杂的微生物区系,包括真核微生物鞭毛虫和原核生物,细菌及古细菌。低等白蚁的后肠以特别膨大的囊形胃及其氢氧浓度的明显梯度分布和丰富的微生物区系为特征,是白蚁进行木质纤维素消化的主要器官。后肠内的鞭毛虫能将纤维素水解并发酵为乙酸,二氧化碳和氢,为白蚁提供营养和能源。系统发育研究表明,低等白蚁肠道共生细菌的主要类群为白蚁菌群1、螺旋体、拟杆菌,低G C mol%含量的革兰氏阳性菌和紫细菌等。而古细菌主要为甲烷短杆菌属的产甲烷菌。共生原核生物与二氧化碳的还原和氮的循环等代谢有关。但肠道共生微生物的具体功能和作用机制还有待进一步的揭示。     

Signal function of calcium-binding proteins in lower eukaryotes

This review summarizes data on the signaling role of calcium-binding proteins (CaBP) in lower eukaryotes cells. The contributions of calmodulin (CaM)-like proteins, calcium-dependent protein kinases (CDPK), as well as calcineurin B-like phosphatase (CaNB) and some other proteins to Ca(2+)-dependent regulation of cellular functions is considered.     

The nonhistone chromosomal proteins of vertebrate liver and kidney: A comparative study by gel electrophoresis

Summary The nonhistone chromosomal proteins (NHC proteins) probably include enzymes of chromosomal metabolism, general structural proteins, and possibly control elements. In theory, these proteins may have been strongly conserved during evolution, as the histones have. We have used sodium dodecyl sulfate (SDS) disc gel electrophoresis to analyze and compare the NHC proteins of two tissues, liver and kidney, from rat, cat, cow, chicken, turtle, and frog. The gel patterns indicate that the NHC proteins have changed much more during evolution than have the histones; the total pattern of NHC proteins has not been conserved. However, there does appear to be a conservation of a subset of bands for each tissue investigated. Further chemical analysis will be required to establish the significance of the results.Recipient of NIH Career Development Award NIH AI-20388     

Examination of protein sequence homologies: III. Ribosomal protein YS25 fromSaccharomyces cerevisiae and its counterparts fromSchizosaccharomyces pombe,rat liver,andEscherichia coli

Summary The sequences of the ribosomal proteins YS25, SP-S28, RL-S21, and Ec-S6, fromSaccharomyces cerevisiae, Schizosaccharomyces pombe, rat liver, andEscherichia coli, respectively, have been examined using a computer program that searches for homologous tertiary structures. Matrices of comparisons among the eukaryotic sequences show that they match each other sequentially without any internal gaps. The average values of the correlation coefficients obtained from the comparison matrices are higher for the first halves of the sequences than for the latter halves. This result suggests that the first halves of the sequences may represent a more important domain than the latter halves. The comparison matrices between the eukaryotic and bacterial sequences of ribosomal proteins, however, do not show sequentially arranged homology, though there are six well-matching segments arranged in different orders in the two types of sequences. This implies that the eukaryotic sequences of the ribosomal protein were reconstituted by two internal transpositions and six deletions of 4–12 residues each from the ancestral sequence during the divergence between bacterial and eukaryotic genes. These findings may give insight into structural and quantitative studies of evolutionary divergence between eukaryotes and prokaryotes.     

The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids

Abstract Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (α- and β-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-1α, α-tubulin, and β-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of “Plantae” is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.     

Structural comparison of 26S rRNA-binding ribosomal protein L25 from two different yeast strains and the equivalent proteins from three eubacteria and two chloroplasts

Summary The sequences ofSaccharomyces carlsbergensis ribosomal protein (r-protein) SL25^* and its equivalents fromCandida utilis (CL25),Escherichia coli (EL23),Bacillus stearothermophilus (BL23),Mycoplasma capricolum (ML23),Marchantia polymorpha chloroplasts (McpL23), andNicotiana tabacum chloroplasts (NcpL23) were examined using a computer program that evaluates the extent of sequence similarity by calculating correlation coefficients for each pair of residues in two proteins from a number of physical properties of individual amino acids. Comparison matrices demonstrate that the prokaryotic sequences (including McpL23 and NcpL23) can be aligned unambiguously by introducing small internal deletions/insertions at three specific positions. A similar comparison brought to light a clear evolutionary relationship between the prokaryotic and the yeast proteins despite the fact that visual inspection of these sequences revealed only limited similarity. The alignment deduced from this comparison shows the two yeast r-proteins to have acquired a long (50–60 amino acids) N-terminal extension as well as a 13-amino acid-long deletion near the C-terminus. The significance of these findings in terms of the evolution of r-proteins in general and the biological function of various parts of the SL25 protein in particular is discussed.     

Eucaryotic cell components that bind to chlamydial elementary bodies: the histones

HeLa-cell-membrane fractions isolated by sonication as used previously to identify chlamydial adhesins were examined by a blotting technique for binding chlamydial elementary bodies (EB). One HeLa cell protein with apparent molecular mass of 32 kDa was found to bind native EB. A monoclonal antibody (mAb) raised against this chlamydial binding host-cell protein reacted with eucaryotic histones. Histone fractions were capable of binding EB in an ELISA assay and histone H1 was identified as the chlamydial-binding host cell protein in the Hela cell membrane fraction. Probing with specific mAbs against histone H3 and DNA confirmed that chromatin components were present in the host-cell membrane extract. These data suggest that the HeLa-cell-binding chlamydial proteins were previously identified by their reaction with chromatin and not with membrane components.     

The molecular evolution of cytochrome c in eukaryotes

Summary Using many more cytochrome sequences than previously available, we have confirmed: 1, the eukaryotic cytochromes c diverged from a common ancestor; 2, the ancestral eukaryotic cytochrome c was not greatly different in character from those present today; 3, fixations are non-randomly distributed among the codons, there being evidence for at least four classes of variability; 4, there are similar classes of variability when the data are considered according to the nucleotide position within the codon; 5, the number of covarions (concomitantly variable codons) in mammalian cytochrome c genes is about 12 and the same value has been obtained for dicotyledonous plants as well; 6, all of the hyper- and most highly variable codons are for external residues, nearly 60 per cent of the invariable codons are for internal residues and nearly half of the codons for internal residues are invariable; 7, the first nucleotide position of a codon is more likely and the second position less likely to fix mutations than would be expected on the basis of the number of ways that alternative amino acids can be reached; 8, the character of nucleotide replacements is enormously non-random, with GA interchanges representing 42% of those observed in the first nucleotide position, but the observation does not stem from a bias in the DNA strand receiving the mutation, nor from the presence of a compositional equilibrium, nor from a bias in the frequency with which different nucleotides mutate, but rather from a bias in the acceptability of an alternative nucleotide as circumscribed by the functional acceptability of the new amino acid encoded; and 9, the unit evolutionary period is approximately 150 million years/observable (amino acid changing) nucleotide replacement/cytochrome c covarion in two diverging lines.Wherever non-randomness has been observed, it has always been consistent with the consideration that an alternative amino acid at any location is more likely to be acceptable the more closely it resembles the present amino acid in its physico-chemical properties.Finally, in no case did the a priori assumption of a biologically realistic phylogeny lead to any observations or conclusions that were in any way significantly different from those obtained when the phylogeny was based solely upon the sequences, proving that the earlier results were not a consequence of some internal circularity.     

The effects of histones H1o,H5 and HMG proteins on cell division of cultured murine erythroleukemia cells

Summary In the present study the effect of histones H1^o and H5, and the nonhistone chromatin proteins HMG 1, 2, 14 and 17 (the high mobility group proteins), as well as the acidic peptide fragments of HMG 1 and 2 and polyglutamate, on cell division and differentation of cultured murine erythroleukemia (Friend) cells has been investigated. It was found that histones H1^o and H5, the acidic peptide fragments of HMG 1 and 2, HMG 14 and 17 and sodium polyglutamate stimulated cell division at a concentration of 10 g/ml. None of the H1^o, H5 or HMG protein preparations induced hemoglobin synthesis, as judged by benzidine staining.     

Functional homologies of acidic chromatin proteins in higher and lower eukaryotes

Within a specific fraction of acidic chromatin-associated proteins from HeLa and the lower eukaryote Physarum polycephalum numerous similarities exist. Several of the similar polypeptides in both cell types are synthesized and appear in the residual chromatin material while still others disappear in response to starvation, a common and universal stimulus. Proteins which incorporate no radioactive amino acids during starvation and ultimately disappear from the residual chromatin material are resynthesized upon refeeding. This resynthesis must be complete before mitosis will again occur. These observations suggest that within the complement of acidic chromatin proteins functional homologies exist in diverse eukaryotes.     

Origin and evolution of chromosomal sperm proteins

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a “vertical” transition from a histone to a protamine‐like and finally protamine types (H → PL → P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine‐like (PL)‐ and protamine (P)‐types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution.     

Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins

The function of small ubiquitin-like modifier (SUMO)-binding proteins is key to understanding how SUMOylation regulates cellular processes. We identified two related Schizosaccharomyces pombe proteins, Rfp1 and Rfp2, each having an N-terminal SUMO-interacting motif (SIM) and a C-terminal RING-finger domain. Genetic analysis shows that Rfp1 and Rfp2 have redundant functions; together, they are essential for cell growth and genome stability. Mammalian RNF4, an active ubiquitin E3 ligase, is an orthologue of Rfp1/Rfp2. Rfp1 and Rfp2 lack E3 activity but recruit Slx8, an active RING-finger ubiquitin ligase, through a RING-RING interaction, to form a functional E3. RNF4 complements the growth and genomic stability defects of rfp1rfp2, slx8, and rfp1rfp2slx8 mutant cells. Both the Rfp-Slx8 complex and RNF4 specifically ubiquitylate artificial SUMO-containing substrates in vitro in a SUMO binding-dependent manner. SUMOylated proteins accumulate in rfp1rfp2 double-null cells, suggesting that Rfp/Slx8 proteins may promote ubiquitin-dependent degradation of SUMOylated targets. Hence, we describe a family of SIM-containing RING-finger proteins that potentially regulates eukaryotic genome stability through linking SUMO-interaction with ubiquitin conjugation.     

The evolution of angiosperm seed proteins: A methionine-rich legumin subfamily present in lower angiosperm Clades

Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms. Correspondence to: H. Fischer     

S100 proteins in mouse and man: from evolution to function and pathology (including an update of the nomenclature)

The S100 protein family is the largest subgroup within the superfamily of proteins carrying the Ca2+-binding EF-hand motif. Despite their small molecular size and their conserved functional domain of two distinct EF-hands, S100 proteins developed a plethora of tissue-specific intra- and extracellular functions. Accordingly, various diseases such as cardiomyopathies, neurodegenerative and inflammatory disorders, and cancer are associated with altered S100 protein levels. Here, we review the different S100 protein functions and related diseases from an evolutionary point of view. We analyzed the structural variations, which are the basis of functional diversification, as well as the genomic organization of the S100 family in human and compared it with the S100 repertoires in mouse and rat. S100 genes and proteins are highly conserved between the different mammalian species. Moreover, we identified evolutionary related subgroups of S100 proteins within the three species, which share functional similarity and form subclusters on the genomic level. The available S100-specific mouse models are summarized and the consequences of our results are discussed with regard to the use of genetically engineered mice as human disease models. An update of the S100 nomenclature is included, because some of the recently identified S100 genes and pseudogenes had to be renamed.     

Alternative glycosylation modulates function of IgG and other proteins — Implications on evolution and disease

Background

Nearly all membrane and secreted proteins, as well as numerous intracellular proteins are glycosylated. However, contrary to proteins which are defined by their individual genetic templates, glycans are encoded in a complex dynamic network of hundreds of genes which participate in the complex biosynthetic pathway of protein glycosylation.

Scope of review

This review summarizes present knowledge about the importance of alternative glycosylation of IgG and other proteins.

Major conclusions

Numerous proteins depend on correct glycosylation for proper function. Very good example for this is the alternative glycosylation of IgG whose effector functions can be completely changed by the addition or removal of a single monosaccharide residue from its glycans.

General significance

The change in the structure of a protein requires mutations in DNA and subsequent selection in the next generation, while even slight alterations in activity or intracellular localization of one or more biosynthetic enzymes are sufficient for the creation of novel glycan structures, which can then perform new functions. Glycome composition varies significantly between individuals, which makes them slightly or even significantly different in their ability to execute specific molecular pathways with numerous implications for development and progression of various diseases. This article is part of a Special Issue entitled Glycoproteomics.     

Bacterial-like PPP protein phosphatases: Novel sequence alterations in pathogenic eukaryotes and peculiar features of bacterial sequence similarity

Reversible phosphorylation is a widespread modification affecting the great majority of eukaryotic cellular proteins, and whose effects influence nearly every cellular function. Protein phosphatases are increasingly recognized as exquisitely regulated contributors to these changes. The PPP (phosphoprotein phosphatase) family comprises enzymes, which catalyze dephosphorylation at serine and threonine residues. Nearly a decade ago, “bacterial-like” enzymes were recognized with similarity to proteins from various bacterial sources: SLPs (Shewanella-like phosphatases), RLPHs (Rhizobiales-like phosphatases), and ALPHs (ApaH-like phosphatases). A recent article from our laboratory appearing in Plant Physiology characterizes their extensive organismal distribution, abundance in plant species, predicted subcellular localization, motif organization, and sequence evolution. One salient observation is the distinct evolutionary trajectory followed by SLP genes and proteins in photosynthetic eukaryotes vs. animal and plant pathogens derived from photosynthetic ancestors. We present here a closer look at sequence data that emphasizes the distinctiveness of pathogen SLP proteins and that suggests that they might represent novel drug targets. A second observation in our original report was the high degree of similarity between the bacterial-like PPPs of eukaryotes and closely related proteins of the “eukaryotic-like” phyla Myxococcales and Planctomycetes. We here reflect on the possible implications of these observations and their importance for future research.