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[The phylogeny of the Trypanosomatidae: the molecular and morphological approaches].

The results of comparative analysis of two phylogenetic trees of the trypanosomatids based on morphological and molecular characters are discussed. The morphological dendrogram was based on 33 ultrastructural characters, 6 light microscope characteristics and 8 biological characters. Molecular UPGMA dendrogram depicting differences (Dice distance) between examined trypanosomatids is based on the universally primed PCR polymorphisms. The general topology of both dendrograms are similar, with the Trypanosoma at the base. The genus Wallaceina appears to be monophyletic. In a contrary, the genera Leptomonas, Crithidia and Herpetomonas look like artificial groups according to both methods used. The cyst-forming homoxenous trypanosomatids from insects represent a monophyletic clade, which seems to be a separate genus. Two species of within genus Wallaceina are arranged as a separate subgenus.

Animals↗

PubMed2005

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

BACKGROUND: Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets. RESULTS: transAlign is an open-source Perl script that aligns protein-coding DNA sequences via their amino-acid translations to take advantage of the superior multiple-alignment capabilities and speed of an amino-acid alignment. It operates by translating each DNA sequence into its corresponding amino-acid sequence, passing the entire matrix to ClustalW for alignment, and then back-translating the resulting amino-acid alignment to derive the aligned DNA sequences. In the translation step, transAlign determines the optimal orientation and reading frame for each DNA sequence according to the desired genetic code. It also checks for apparent frame shifts in the DNA sequences and can handle frame-shifted sequences in one of three ways (delete, align as amino acids regardless, or profile align as DNA). As a set of comparative benchmarks derived from six protein-coding genes for mammals shows, the strategy implemented in transAlign always improves the speed and usually the apparent accuracy of the alignment of protein-coding DNA sequences. CONCLUSION: transAlign represents one of few full and cross-platform implementations of the concept of translated alignments. Both the advantages accruing from performing a translated alignment and the suite of user-definable options available in the program mean that transAlign is ideally suited for large-scale automated alignments of very large and/or very numerous protein-coding DNA data sets. However, the good performance offered by the program also translates to the alignment of any set of protein-coding sequences. transAlign, including the source code, is freely available at http://www.tierzucht.tum.de/Bininda-Emonds/ (under "Programs").

Algorithms↗

PubMed1997

The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa.

Hepatitis C virus (HCV) genotype 5a is the predominant genotype in southern Africa with a high prevalence amongst infected blood donors from areas in South Africa. We have determined the nucleotide sequence corresponding to the complete coding region of an HCV isolate, EUH1480, previously classified as genotype 5a, from an Edinburgh haemophiliac. The sequence contained a single open reading frame (ORF) coding for a polyprotein of 3014 amino acids. Comparison with the polyprotein sequences from other HCV genotypes, where the ORF varies from 3008 to 3037 amino acids, showed the observed variation in size was due to differences in lengths of the envelope 2 and the nonstructural 5A proteins. The sequence divergence of HCV genotype 5 ranged from 29.4% nucleotide differences (24.91% amino acid differences) compared with genotype 1c to 32.5% nucleotide differences (30.3% amino acid differences) compared with 2a. Phylogenetic analysis of the available full length nucleotide sequences showed EUH1480 to form a branch distinct from the other HCV types, confirming the classification of type 5a as a separate genotype.

Amino Acid Sequence↗

PubMed2006

Microbial diversity in hypersaline wastewater: the example of tanneries.

In contrast to conventional wastewater treatment plants and saline environments, little is known regarding the microbial diversity of hypersaline wastewater. In this study, the microbial communities of a hypersaline tannery effluent, and those of three treatment systems operating with the tannery effluent, were investigated using 16S rDNA phylogenetic markers. The comparative analysis of 377 bacterial sequences revealed the high diversity of this type of hypersaline environment, clustering within 193 phylotypes (> or = 97% similarity) and covering 14 of the 52 divisions of the bacterial domain, i.e. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chlorobi, Planctomycetes, Spirochaetes, Synergistes, Chloroflexi, Thermotogae, Verrucomicrobia, OP3, OP11 and TM7. Most of the phylotypes were related to halophilic and pollutant-degrading bacteria. Using statistical analysis, the diversity of this type of environment was compared to that of other environmental samples selected on the basis of their salinity, oxygen content and organic load.

Bacteria↗

PubMed2026

Molecular epidemiology and genomic characteristics of clinical Acinetobacter baumannii isolates from patients with hospital-acquired pneumonia in China, 2019-2020: a multicentre retrospective study.

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of hospital-acquired pneumonia (HAP) with high mortality. However, large-scale nationwide data of HAP-causing CRAB in China remain limited. METHODS: Here, we performed a nationwide multicentre retrospective study to characterise the molecular epidemiology and genomic features of 802 A. baumannii isolates from patients with HAP across 33 tertiary hospitals in China during 2019-2020. Antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), phylogenetic and comparative genomic analysis were used to investigate molecular epidemiology of HAP-causing CRAB strain. Clinical comparative analyses were carried out on data from 500 patients with HAP stratified by distinct antimicrobial susceptibility and genomic profiles, and a Galleria mellonella infection model was utilised for in vivo virulence assessment. FINDINGS: The overall carbapenem resistance rate of A. baumannii was 82.0% (658/802), with marked regional variations. CRAB exhibited high resistance to conventional agents but remained largely susceptible to polymyxin, tigecycline, cefiderocol and sulbactam-durlobactam. Among enrolled patients, CRAB infection was linked to substantially higher mortality (39.0% vs. 17.5%), and multivariate analysis confirmed ICU admission and advanced age as independent risk factors for patients with CRAB infection. Molecular typing revealed STPas2 (96.2%) as the absolutely predominant type; STOxf208, STOxf195, STOxf540, and STOxf369 were the most prevalent Oxford sequence types with obvious geographic stratification and divergent comorbidity profiles among corresponding patients. A total of 654 CRAB isolates harboured carbapenemase genes, with blaOXA-23 dominating at 98.8%. Genomic analysis revealed lineage-specific features: STOxf208 carried more virulence genes, while STOxf540 harboured a broader antimicrobial resistance genes (ARGs). The STOxf208 clone mainly belonged to KL2 (62.1%) and KL7 (36.8%) serotypes, with KL2 strains possessing richer ARGs and virulence factors, and in vivo virulence assays further validated that KL2 strains possessed higher pathogenicity than KL7 strains. INTERPRETATION: This study demonstrates the extremely high prevalence and clonal dominance of CRAB in Chinese patients with HAP, providing critical evidence for clinical treatment, antimicrobial stewardship, and targeted infection control. FUNDING: National Key Research and Development Program of China (2024YFE0106200), National Natural Science Foundation of China (U22A20338, 82502763, W2621007), Zhejiang Provincial Natural Science Foundation of China (LQN25H190006), Zhejiang Provincial Postdoctoral Science Foundation (ZJ2025058).

Acinetobacter baumannii↗

PubMed2005

Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms.

The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt) sequences of the VHSV glycoprotein (G) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G-gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-length G-gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes. Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G-gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis was shown to approximate the level of genetic discrimination obtained by other, more labour-intensive, molecular techniques such as the ribonuclease protection assay or sequence analysis. In addition, 37 previously uncharacterised isolates from diverse sources were assigned to specific genotypes. While the assay was able to distinguish between marine and continental isolates of VHSV, the differences did not correlate with the pathogenicity of the isolates.

Animals↗

PubMed1999

JIL-1: a novel chromosomal tandem kinase implicated in transcriptional regulation in Drosophila.

We have cloned and characterized JIL-1, a novel tandem kinase in Drosophila that associates with the chromosomes throughout the cell cycle. Antibody staining and live imaging of JIL-1-GFP transgenic flies show that JIL-1 localizes to the gene-rich interband regions of larval polytene chromosomes and is upregulated almost 2-fold on the hypertranscribed male X chromosome compared to autosomes. Phylogenetic analysis suggests that JIL-1 together with human MSKs defines a separate family of tandem kinases. That JIL-1 is a functional kinase was demonstrated by autophosphorylation and phosphorylation of histone H3 in vitro. Based on these findings, we propose that JIL-1 may play a role in transcriptional control potentially by regulating chromatin structure.

Amino Acid Sequence↗

PubMed2004

Sutterella stercoricanis sp. nov., isolated from canine faeces.

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (= CCUG 47620T = CIP 108024T).

Alcaligenaceae↗

PubMed2005

Slackia faecicanis sp. nov., isolated from canine faeces.

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-positive, rod-shaped bacterium that was isolated from dog faeces. The bacterium grew under strictly anaerobic conditions, was asaccharolytic, and possessed a relatively high G + C content of 61 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium was a member of the family Coriobacteriaceae and represents a hitherto unknown subline within the genus Slackia. Based on the presented findings, a novel species, Slackia faecicanis sp. nov., is described. The type strain of Slackia faecicanis is 5WC12(T) (= CCUG 48399(T) = CIP 108281(T)).

Actinobacteria↗

PubMed2005

Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor.

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61T and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus Rhizobium comprising the type strains of Rhizobium giardinii, Rhizobium radiobacter, Rhizobium rubi, Rhizobium larrymoorei, Rhizobium vitis, Rhizobium undicola, Rhizobium loessense, Rhizobium galegae and Rhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0.6-0.7x1.1-1.3 microm), with peritrichous flagella. The DNA G+C content is 60.1-60.9 mol%. Cellular fatty acids are C(16 : 0) (2.2-3.3 %), C(18 : 0) (2.1-3.2 %), C(19 : 0) cyclo omega8c (9.9-16.8 %), C(20 : 3)omega6,9,12c (2.7-3.3 %), summed feature 3 (7.2-7.7 %) and summed feature 7 (67.8-73.7 %). The strains formed nodules on a legume plant, Medicago sativa. A nifH gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61T by PCR amplification by using a nifH-specific primer system. Strains L61T and L22 were distinguished from the type strains of recognized Rhizobium species in the same sublineage based on low DNA-DNA hybridization values (2-4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61T and L22 from Rhizobium species in the same sublineage. Based on the results obtained in this study, L61T and L22 are considered to be representatives of a novel species of Rhizobium, for which the name Rhizobium daejeonense sp. nov. is proposed. The type strain is L61T (=KCTC 12121T=IAM 15042T=CCBAU 10050T).

Bioreactors↗

PubMed2006

Azonexus caeni sp. nov., a denitrifying bacterium isolated from sludge of a wastewater treatment plant.

A polyphasic taxonomic study was carried out to determine the taxonomic position of a newly isolated denitrifying bacterium, designated Slu-05T, which had been isolated from sludge from the main aerobic treatment tanks of a municipal sewage treatment plant. Phylogenetic analysis based on comparative 16S rRNA gene sequencing indicated that strain Slu-05T was closely related to Azonexus fungiphilus LMG 19178T (96.4 % sequence similarity), the sole species in the genus Azonexus. Strain Slu-05T comprised Gram-negative, motile, non-spore-forming and slightly curved rods. The predominant respiratory lipoquinone was Q-8. The major fatty acids were C16:1omega7c, C16:0, C18:1 isomers and C10:0 3-OH. The G+C content of the genomic DNA was 65.6 mol%. The results of DNA-DNA hybridization (15.6 %) together with phenotypic determination showed that strain Slu-5T could be distinguished from A. fungiphilus. Moreover, some phenotypic properties concerning enzyme activity, the substrates utilized as carbon sources and growth conditions distinguish strain Slu-5T from A. fungiphilus. On the basis of the results obtained in this study, Slu-05T (=DSM 17719T=KCTC 12530T=CCBAU 10199T) is the type strain of a novel species of Azonexus, for which the name Azonexus caeni sp. nov. is proposed.

Bacterial Typing Techniques↗

PubMed2004

Genetic and phenotypic variations of isolates of shrimp Taura syndrome virus found in Penaeus monodon and Metapenaeus ensis in Taiwan.

Distinct Taura syndrome virus (TSV) isolates were found in Metapenaeus ensis (isolate Tw2KMeTSV), Penaeus monodon (isolate Tw2KPmTSV) and Litopenaeus vannamei (isolate Tw02LvTSV). Nucleotide sequence analysis of these three isolates revealed differences in the TSV structural protein (capsid protein precursor) gene orf2. TSV ORF2 amino acid sequence comparison and phylogenetic analysis suggested a comparatively close relationship between these three Taiwanese isolates and the Hawaiian isolate HI94TSV. In P. monodon specimens that were naturally and experimentally infected with the Tw2KPmTSV isolate, the virus was contained and shrimps showed no clinical signs of infection. However, when P. monodon was challenged with the Tw2KMeTSV isolate, the virus replicated freely. The ORF2 amino acid sequence of the Tw2KMeTSV isolate differed from that of isolate Tw2KPmTSV in four positions and these differences may account for their phenotypic differences, at least in terms of their ability to replicate in specific hosts.

Animals↗

PubMed2002

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional BirA protein, which acts both as a biotin-protein ligase and as a transcriptional repressor of the biotin operon. Little is known about regulation of biotin biosynthesis in other bacteria. Using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the BirA regulon in most available bacterial genomes. Existence of an N-terminal DNA-binding domain in BirA strictly correlates with the presence of putative BirA-binding sites upstream of biotin operons. The predicted BirA-binding sites are well conserved among various eubacterial and archaeal genomes. The possible role of the hypothetical genes bioY and yhfS-yhfT, newly identified members of the BirA regulon, in the biotin metabolism is discussed. Based on analysis of co-occurrence of the biotin biosynthetic genes and bioY in complete genomes, we predict involvement of the transmembrane protein BioY in biotin transport. Various nonorthologous substitutes of the bioC-coupled gene bioH from E. coli, observed in several genomes, possibly represent the existence of different pathways for pimeloyl-CoA biosynthesis. Another interesting result of analysis of operon structures and BirA sites is that some biotin-dependent carboxylases from Rhodobacter capsulatus, actinomycetes, and archaea are possibly coregulated with BirA. BirA is the first example of a transcriptional regulator with a conserved binding signal in eubacteria and archaea.

Archaeal Proteins↗

PubMed2004

Functional characterization of enzymes forming volatile esters from strawberry and banana.

Volatile esters are flavor components of the majority of fruits. The last step in their biosynthesis is catalyzed by alcohol acyltransferases (AATs), which link alcohols to acyl moieties. Full-length cDNAs putatively encoding AATs were isolated from fruit of wild strawberry (Fragaria vesca) and banana (Musa sapientum) and compared to the previously isolated SAAT gene from the cultivated strawberry (Fragaria x ananassa). The potential role of these enzymes in fruit flavor formation was assessed. To this end, recombinant enzymes were produced in Escherichia coli, and their activities were analyzed for a variety of alcohol and acyl-CoA substrates. When the results of these activity assays were compared to a phylogenetic analysis of the various members of the acyltransferase family, it was clear that substrate preference could not be predicted on the basis of sequence similarity. In addition, the substrate preference of recombinant enzymes was not necessarily reflected in the representation of esters in the corresponding fruit volatile profiles. This suggests that the specific profile of a given fruit species is to a significant extent determined by the supply of precursors. To study the in planta activity of an alcohol acyltransferase and to assess the potential for metabolic engineering of ester production, we generated transgenic petunia (Petunia hybrida) plants overexpressing the SAAT gene. While the expression of SAAT and the activity of the corresponding enzyme were readily detected in transgenic plants, the volatile profile was found to be unaltered. Feeding of isoamyl alcohol to explants of transgenic lines resulted in the emission of the corresponding acetyl ester. This confirmed that the availability of alcohol substrates is an important parameter to consider when engineering volatile ester formation in plants.

Acyltransferases↗

PubMed2006

Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.

Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

Amino Acid Sequence↗

PubMed2005

Abyss1: a novel L2-like non-LTR retroelement of the snakelocks anemone (Anemonia sulcata).

Non-LTR retrotransposons are a diverse and taxonomically widely dispersed group of retroelements that can be divided into at least 14 distinguishable clades. Basal metazoans have not been examined in great detail for their retrotransposon content. In order to screen for the presence of reverse transcriptase (RT) related sequences in Cnidaria and Ctenophora, basal phyla of metazoans, PCR with highly degenerate oligonucleotides was performed and an RT-like sequence was identified from the sea anemone species Anemonia sulcata. Further screening identified a related element in another anemone species Actinia equina. Significant homology to non-LTR retrotransposon RTs was observed, particularly to L2-like elements of fish such as Maui. The sequence was not detected among other cnidarians and we have designated the A. sulcata and A. equina elements Abyss1 and Abyss2 respectively. Phylogenetic analysis of Abyss1 compared with members of 14 known non-LTR retroelement clades suggests that the sequence represents a novel L2 element.

Amino Acid Sequence↗

PubMed2006

High degree of conservancy among secreted salivary gland proteins from two geographically distant Phlebotomus duboscqi sandflies populations (Mali and Kenya).

BACKGROUND: Salivary proteins from sandflies are potential targets for exploitation as vaccines to control Leishmania infection; in this work we tested the hypothesis that salivary proteins from geographically distant Phlebotomus duboscqi sandfly populations are highly divergent due to the pressure exerted by the host immune response. Salivary gland cDNA libraries were prepared from wild-caught P. duboscqi from Mali and recently colonised flies of the same species from Kenya. RESULTS: Transcriptome and proteome analysis resulted in the identification of the most abundant salivary gland-secreted proteins. Orthologues of these salivary proteins were identified by phylogenetic tree analysis. Moreover, comparative analysis between the orthologues of these two different populations resulted in a high level of protein identity, including the predicted MHC class II T-cell epitopes from all these salivary proteins. CONCLUSION: These data refute the hypothesis that salivary proteins from geographically distinct populations of the same Phlebotomus sandfly species are highly divergent. They also suggest the potential for using the same species-specific components in a potential vector saliva-based vaccine.

Africa, Eastern↗

PubMed2003

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.

BACKGROUND: Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. Here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities. RESULTS: Since a substantial number of operons have been identified experimentally in only a few model bacteria, evolutionarily conserved gene strings were analyzed as surrogates of operons. The phylogenetic affinities within these predicted operons were assessed first by sequence similarity analysis and then by phylogenetic analysis, including statistical tests of tree topology. Numerous cases of apparent horizontal transfer of entire operons were detected. However, it was shown that apparent horizontal transfer of individual genes or arrays of genes within operons is not uncommon either and results in xenologous gene displacement in situ, that is, displacement of an ancestral gene by a horizontally transferred ortholog from a taxonomically distant organism without change of the local gene organization. On rarer occasions, operons might have evolved via independent assembly, in part from horizontally acquired genes. CONCLUSIONS: The discovery of in situ gene displacement shows that combination of rampant horizontal gene transfer with selection for preservation of operon structure provides for events in prokaryotic evolution that, a priori, seem improbable. These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level.

Alkyl and Aryl Transferases↗