Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.     

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

Thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rRNA and other phylogenetic trees. No biochemical or molecular markers are known that clearly distinguish the species from this phylum from all other bacteria. The taxonomic/evolutionary relationships within this phylum, which consists of a single family, are also unclear. We report detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal as well as other conserved proteins that identify a number of distinct clades within this phylum. Additionally, comprehensive analyses of protein sequences from Thermotogae genomes have identified >60 Conserved Signature Indels (CSI) that are specific for the Thermotogae phylum or its different subgroups. Eighteen CSIs in important proteins such as PolI, RecA, TrpRS and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in various Thermotogae species and provide molecular markers for the phylum. Many CSIs were specific for a number of Thermotogae subgroups. Twelve of these CSIs were specific for a clade consisting of various Thermotoga species except Tt. lettingae, which was separated from other Thermotoga species by a long branch in phylogenetic trees; Fourteen CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and eight additional CSIs were specific for the genus Thermosipho. In addition, the existence of a clade consisting of the deep branching species Petrotoga mobilis, Kosmotoga olearia and Thermotogales bacterium mesG1 was supported by seven CSIs. The deep branching of this clade was also supported by a number of CSIs that were present in various Thermotogae species, but absent in this clade and all other bacteria. Most of these clades were strongly supported by phylogenetic analyses based on two datasets of protein sequences and they identify potential higher taxonomic grouping (viz. families) within this phylum. We also report 16 CSIs that are shared by either some or all Thermotogae species and some species from other taxa such as Archaea, Aquificae, Firmicutes, Proteobacteria, Deinococcus, Fusobacteria, Dictyoglomus, Chloroflexi and eukaryotes. The shared presence of some of these CSIs could be due to lateral gene transfers between these groups. However, no clear preference for any particular group was observed in this regard. The molecular probes based on different genes/proteins, which contain these Thermotogae-specific CSIs, provide novel and highly specific means for identification of both known as well as previously unknown Thermotogae species in different environments. Additionally, these CSIs also provide valuable tools for genetic and biochemical studies that could lead to discovery of novel properties that are unique to these bacteria.     

Molecular signatures for the Crenarchaeota and the Thaumarchaeota

Crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of Archaea called the Thaumarchaeota. However, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the Crenarchaeota. In addition, their relationships to deep-branching archaeal lineages are unclear. We report here detailed analyses of protein sequences from Crenarchaeota and Thaumarchaeota that have identified many conserved signature indels (CSIs) and signature proteins (SPs) (i.e., proteins for which all significant blast hits are from these groups) that are specific for these archaeal groups. Of the identified signatures 6 CSIs and 13 SPs are specific for the Crenarchaeota phylum; 6 CSIs and >250 SPs are uniquely found in various Thaumarchaeota (viz. Cenarchaeum symbiosum, Nitrosopumilus maritimus and a number of uncultured marine crenarchaeotes) and 3 CSIs and ~10 SPs are found in both Thaumarchaeota and Crenarchaeota species. Some of the molecular signatures are also present in Korarchaeum cryptofilum, which forms the independent phylum Korarchaeota. Although some of these molecular signatures suggest a distant shared ancestry between Thaumarchaeota and Crenarchaeota, our identification of large numbers of Thaumarchaeota-specific proteins and their deep branching between the Crenarchaeota and Euryarchaeota phyla in phylogenetic trees shows that they are distinct from both Crenarchaeota and Euryarchaeota in both genetic and phylogenetic terms. These observations support the placement of marine mesophilic archaea into the separate phylum Thaumarchaeota. Additionally, many CSIs and SPs have been found that are specific for different orders within Crenarchaeota (viz. Sulfolobales—3 CSIs and 169 SPs, Thermoproteales—5 CSIs and 25 SPs, Desulfurococcales—4 SPs, and Sulfolobales and Desulfurococcales—2 CSIs and 18 SPs). The signatures described here provide novel means for distinguishing the Crenarchaeota and the Thaumarchaeota and for the classification of related and novel species in different environments. Functional studies on these signature proteins could lead to discovery of novel biochemical properties that are unique to these groups of archaea.     

Molecular clocks, molecular phylogenies and the origin of phyla

Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla .     

8株光合细菌的鉴定及其系统进化关系分析

目的为8株光合细菌(photosynthetic bacteria,PSB)作为益生菌株提供系统资料。方法用常规方法对8株PSB菌株的形态、培养特性及生理生化特征进行鉴定,同时定性分析菌株产生的类胡萝卜素和CoQ,测定菌株16S DNA序列并分析其系统进化关系,在GenBank中获取了8个16S DNA序列号。结果菌株鉴定结果表明:菌株2C、2c和13ing为沼泽红假单胞菌,Ga、Il106、WS8N为类球红细菌,MT1131为荚膜红细菌,rub为深红红螺菌。基于菌株16S DNA序列的系统进化树显示,同一种菌并不总是聚为一簇,但相隔较近;种属完全不同的菌株,尽管序列相似性高达97%以上,在系统进化树上相隔较远。结论8株PSB菌株的鉴定和系统进化关系分析结果为后续研究提供了背景资料,同时菌株在GenBank中获得的16S DNA序列号为菌株作上了生物标记,也为菌株的产权保护提供了依据。     

光合细菌培养条件优化的研究

摘要：目的 对光合细菌的培养条件进行优化,优选出更合适的培养基及光合细菌的初始接入量。方法 采用正交试验设计研究培养基中乙酸钠、硫酸铵和酵母膏3个因子对光合细菌生长的影响,以及考察5%、10%、15%和20%不同接菌量的影响,通过测定波长660 nm下菌液的紫外吸光度从而体现光合细菌的生长状况。结果 乙酸钠4.0 g、硫酸铵0.5 g、酵母膏2.0 g为培养基的优化配方,10%的接菌量为最佳。其中乙酸钠对光合细菌生长影响最大。结论 本研究为快速培养高活性的光合细菌奠定了理论基础。     

Value of heterogeneity of bacteria population created by the process of dissociation for the growth of purple photosynthetic bacteria in their natural habitat

For the first time, R- and M-dissociants were isolated from the population of purple phototrophic bacterium Rhodobacter capsulatus, and their growth under different luminance and aeration conditions was studied. Earlier, similar experiments were conducted with R- and M-dissociants of Rhodobacter sphaeroides. The physiological-biochemical differences of connatural bacterial species correlate with the distinctions of their inhabitation: Rhb.spheroides isolated from the soil is characterized by low speed of growth along with the ability to grow in dark and aerobiotic places demonstrated only by M-dissociant, which offers this species an advantage in adaptation for limited and heterogeneity space. Being extracted from the water, rapidly growing Rhb. capsulatus is better adapted for habitation at a free space.     

DNA signatures for detecting genetic engineering in bacteria

Using newly designed computational tools we show that, despite substantial shared sequences between natural plasmids and artificial vector sequences, a robust set of DNA oligomers can be identified that can differentiate artificial vector sequences from all available background viral and bacterial genomes and natural plasmids. We predict that these tools can achieve very high sensitivity and specificity rates for detecting new unsequenced vectors in microarray-based bioassays. Such DNA signatures could be important in detecting genetically engineered bacteria in environmental samples.     

By their genes ye shall know them: genomic signatures of predatory bacteria

Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,'' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria.     

黄瓜根际重要病原与其拮抗菌消长规律的研究

研究了4个不同黄瓜品种根际两类重要土传植物病原菌(Pythiumspp.和Fusariumoxysporum f.sp.cucumerinum)的种群动态变化.结果表明,同一品种不同生长期间种群数有差异,与通常的发病规律相吻合.统计分析可见,腐霉种群和尖孢镰刀菌黄瓜专化型种群品种间差异极显著(F=495.54>F_0.01=7.59;F=2355.57>F_0.01=7.59).整个生育期,所有黄瓜品种种群数极显著地高于其它时期的腐霉种群数,结主蔓瓜期镰刀菌种群数极显著地高于其它时期的镰刀菌种群数.同时,2种病原菌与其拮抗菌均呈较密切的正相关关系,相关系数分别为0.95和0.81.     

An efficient mutational method for photosynthetic bacteria

The pigment and auxotrophic mutants of Rhodobacter sphaeroides Y6 were obtained by treatment with ethyl methanesulfonate (EMS) followed by lithium chloride (LiCI). Treatment with 0.081 M EPS and subsequent treatment with 0.071 M LiCI resulted in 12% higher frequency of pigment mutations than application of 0.081 M EMS alone; the frequency of auxotrophic mutations increased 2.5-fold when treatment with lithium chloride was applied. A blue shift 10 nm was recorded in the absorption spectrum of carotenoids form YM5-3 green mutant; considerable accumulation of neurosporine was revealed by HPLC and mass spectrometry. The method is efficient for isolating mutants of photosynthetic bacteria.     

Molecular signatures for the phylum Synergistetes and some of its subclades

Species belonging to the phylum Synergistetes are poorly characterized. Though the known species display Gram-negative characteristics and the ability to ferment amino acids, no single characteristic is known which can define this group. For eight Synergistetes species, complete genome sequences or draft genomes have become available. We have used these genomes to construct detailed phylogenetic trees for the Synergistetes species and carried out comprehensive analysis to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences that are specific for either all Synergistetes or some of their sub-groups. We report here identification of 32 CSIs in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert within the RpoC protein, that are present in various Synergistetes species, but except for isolated bacteria, these CSIs are not found in the protein homologues from any other organisms. These CSIs provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria. The large numbers of other CSIs discovered in this work provide valuable information that supports and consolidates evolutionary relationships amongst the sequenced Synergistetes species. Of these CSIs, seven are specifically present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a cladal relationship among them, which is also strongly supported by phylogenetic trees. A further 15 CSIs that are only present in Jonquetella and Pyramidobacter indicate a close association between these two species. Additionally, a previously described phylogenetic relationship between the Aminomonas and Thermanaerovibrio species was also supported by 9 CSIs. The strong relationships indicated by the indel analysis provide incentives for the grouping of species from these clades into higher taxonomic groups such as families or orders. The identified molecular markers, due to their specificity for Synergistetes and presence in highly conserved regions of important proteins suggest novel targets for evolutionary, genetic and biochemical studies on these bacteria as well as for the identification of additional species belonging to this phylum in different environments.     

Aerobiosis and the hemoprotein content of photosynthetic bacteria

Summary Rhodospirillum rubrum and Rhodopseudomonas spheroides, grown under various degrees of illumination, aeration, and iron deprivation, have been assayed for their content of cytochrome c, RHP, catalase, total iron, bacteriochlorophyll, and carotenoids.Concentrations of bacteriochlorophyll and carotenoids were consistent with the findings of Cohen-Bazire et al. (1957).Total iron content, which ranged from 0.017 to 0.04% of the dry weight, reflected the content of the principal hemoproteins but exceeded the amount of iron in these hemoproteins.The catalase content of R. rubrum, on a dry weight basis, was 0.0005% for cells grown anaerobically in the light, and 0.0028% for cells grown in darkness with vigorous aeration; that of Rps. spheroides was 0.006% and 0.25%, respectively. The catalase content in both species rose with increasingly vigorous aeration.Cytochrome c in both species, and RHP in R. rubrum, attained the same levels in cells grown under vigorous aeration as in cells grown anaerobically in the light. In cells grown under limited aeration the levels of these substances were about 50% higher. In Rps. spheroides the RHP content was greatest in cells grown anaerobically, falling under gentle aeration and declining further under more vigorous aeration.Iron deficiency caused a decrease in the catalase content of cells grown anaerobically in the light but not in cells grown aerobically. The content of cytochrome c and of RHP was diminished by iron depletion in aerobic cultures, but not in anaerobic cultures.operated by Union Carbide Corporation for the U.S.Atomic Rnergy Commission.     

An efficient mutational method for photosynthetic bacteria

The pigment and auxotrophic mutants of Rhodobacter sphaeroides Y6 were obtained by treatment with ethyl methanesulfonate (EMS) followed by lithium chloride (LiCl). Treatment with 0.081 MEMS and subsequent treatment with 0.071 M LiCl resulted in 12% higher frequency og than that by 0.081 mol/L EMS alone, and the same frequency of pigment mutations than application of 0.081 M EMS alone; the frequency of auxotrophic mutations increased 2.5-fold when treatment with lithium chloride was applied. A blue shift by 10 nm was recorded in the absorption spectrum of carotenoids form YM5-3 green mutant; considerable accumulation of neurosporine was revealed by HPLC and mass spectrometry. The method is efficient for isolating the mutants of photosynthetic bacteria. Published in Russian in Mikrobiologiya, 2006, Vol. 75, No. 6, pp. 758–764. The text was submitted by the authors in English.     

Fluorescence induction of photosynthetic bacteria

The kinetics of bacteriochlorophyll fluorescence in intact cells of the purple nonsulfur bacterium Rhodobacter sphaeroides were measured under continuous and pulsed actinic laser diode (808 nm wavelength and maximum 2 W light power) illumination on the micro- and millisecond timescale. The fluorescence induction curve was interpreted in terms of a combination of photochemical and triplet fluorescence quenchers and was demonstrated to be a reflection of redox changes and electron carrier dynamics. By adjustment of the conditions of single and multiple turnovers of the reaction center, we obtained 11 ms^–1 and 120 μs^–1 for the rate constants of cytochrome c₂³⁺ detachment and cyclic electron flow, respectively. The effects of cytochrome c₂ deletion and chemical treatments of the bacteria and the advantages of the fluorescence induction study on the operation of the electron transport chain in vivo were discussed.