Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments

Sergey V Tarlachkov; Taras V Shevchuk; Maria del Carmen Montero-Calasanz; Irina P Starodumova

doi:10.1093/bioinformatics/btz840

Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments

Bioinformatics ◽

10.1093/bioinformatics/btz840 ◽

2019 ◽

Vol 36 (6) ◽

pp. 1668-1672 ◽

Cited By ~ 1

Author(s):

Sergey V Tarlachkov ◽

Taras V Shevchuk ◽

Maria del Carmen Montero-Calasanz ◽

Irina P Starodumova

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Sodium Pump ◽

Supplementary Information ◽

Ecological Niches ◽

Aquatic Environments ◽

Proton Pumps ◽

Supplementary Data ◽

The Family

Abstract Motivation A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions. Results This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family. Supplementary information Supplementary data are available at Bioinformatics online.

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EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

Bioinformatics ◽

10.1093/bioinformatics/btz706 ◽

2019 ◽

Author(s):

Marina Marcet-Houben ◽

Toni Gabaldón

Keyword(s):

Secondary Metabolism ◽

Computational Prediction ◽

Gene Clusters ◽

Supplementary Information ◽

Supplementary Data ◽

Automated Inference ◽

Or Gene ◽

Conserved Gene ◽

Genome Comparisons

Abstract Motivation The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. Results We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. Availability and implementation https://github.com/Gabaldonlab/EvolClust/. Supplementary information Supplementary data are available at Bioinformatics online.

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Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites

Bioinformatics ◽

10.1093/bioinformatics/btaa492 ◽

2020 ◽

Vol 36 (15) ◽

pp. 4263-4268

Author(s):

Zijie Shen ◽

Quan Zou

Keyword(s):

Machine Learning ◽

Amino Acids ◽

Transcription Factors ◽

Machine Learning Techniques ◽

Supplementary Information ◽

Analysis Process ◽

Learning Techniques ◽

Key Factor ◽

Learning Analysis

Abstract Motivation Methylation and transcription factors (TFs) are part of the mechanisms regulating gene expression. However, the numerous mechanisms regulating the interactions between methylation and TFs remain unknown. We employ machine-learning techniques to discover the characteristics of TFs that bind to methylation sites. Results The classical machine-learning analysis process focuses on improving the performance of the analysis method. Conversely, we focus on the functional properties of the TF sequences. We obtain the principal properties of TFs, namely, the basic polar and hydrophobic Ile amino acids affecting the interaction between TFs and methylated DNA. The recall of the positive instances is 0.878 when their basic polar value is >0.1743. Both basic polar and hydrophobic Ile amino acids distinguish 74% of TFs bound to methylation sites. Therefore, we infer that basic polar amino acids affect the interactions of TFs with methylation sites. Based on our results, the role of the hydrophobic Ile residue is consistent with that described in previous studies, and the basic polar amino acids may also be a key factor modulating the interactions between TFs and methylation. Supplementary information Supplementary data are available at Bioinformatics online.

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TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T cell receptor α and β chains

Bioinformatics ◽

10.1093/bioinformatics/btab573 ◽

2021 ◽

Author(s):

Anja Mösch ◽

Dmitrij Frishman

Keyword(s):

Amino Acids ◽

T Cell ◽

T Cell Receptor ◽

Mrna Level ◽

Cell Receptor ◽

Supplementary Information ◽

Supplementary Data ◽

Β Chain ◽

Complementarity Determining Region

Abstract Summary The ability of a T cell to recognize foreign peptides is defined by a single α and a single β hypervariable complementarity determining region (CDR3), which together form the T cell receptor (TCR) heterodimer. In ∼30%-35% of T cells, two α chains are expressed at the mRNA level but only one α chain is part of the functional TCR. This effect can also be observed for β chains, although it is less common. The identification of functional α/β chain pairs is instrumental in high-throughput characterization of therapeutic TCRs. TCRpair is the first method that predicts whether an α and β chain pair forms a functional, HLA-A*02:01 specific TCR without requiring the sequence of a recognized peptide. By taking additional amino acids flanking the CDR3 regions into account, TCRpair achieves an AUC of 0.71. Availability TCRpair is implemented in Python using TensorFlow 2.0 and is freely available at https://www.github.com/amoesch/TCRpair Supplementary information Supplementary data are available at Bioinformatics online.

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Transcriptional Analysis of Complementary Sense Genes in Spinach curly top virus and Functional Role of C2 in Pathogenesis

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-20-2-0194 ◽

2007 ◽

Vol 20 (2) ◽

pp. 194-206 ◽

Cited By ~ 29

Author(s):

Surendranath Baliji ◽

Janet Sunter ◽

Garry Sunter

Keyword(s):

Amino Acids ◽

Symptom Severity ◽

Functional Role ◽

Mutant Virus ◽

Transcriptional Analysis ◽

Beet Curly Top Virus ◽

The Family ◽

Virion Sense ◽

Complementary Sense

Spinach curly top virus (SCTV), the fifth characterized Curtovirus species belonging to the family Geminiviridae, is an agriculturally significant plant pathogen representing an emerging disease threat in the southern United States. The SCTV genome comprises a single DNA chromosome of approximately 3.0 kb, with the potential to code for seven proteins larger than 10 kDa but which relies extensively on the host for replication and transcription of its genome. In this study, we have identified viral and complementary sense transcripts in SCTV-infected plants, confirming a bidirectional transcription strategy for SCTV. The most abundant RNA maps to the virion sense (1.1-kb transcript) and is comparable in size and location to that observed in Beet curly top virus (BCTV). Two complementary sense transcripts (1.7 and 0.7 kb) were identified in SCTV-infected plants. The large, 1.7-kb transcript is comparable in size and position to that identified in BCTV and several begomoviruses and most likely encodes the C1 protein. Both complementary sense RNAs could potentially direct expression of C2 and C3 from polycistronic mRNAs. A mutation in the C2 gene of SCTV results in expression of a truncated protein of 38 amino acids that is capable of interacting with two cellular kinases, AKIN11 and ADK2, and the resulting mutant virus remains highly infectious. A second mutant virus can only express the first three amino acids of the C2 protein and is unable to interact with the same kinases. However, this mutant virus still remains infectious, although a reduction in infectivity and symptom severity was seen in both Arabidopsis and spinach. A possible relationship between the interaction of C2 with AKIN11 and ADK2 and disease severity is presented.

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Bacteriophage Diversity in the North Sea

Applied and Environmental Microbiology ◽

10.1128/aem.64.11.4128-4133.1998 ◽

1998 ◽

Vol 64 (11) ◽

pp. 4128-4133 ◽

Cited By ~ 121

Author(s):

Antje Wichels ◽

Stefan S. Biel ◽

Hans R. Gelderblom ◽

Thorsten Brinkhoff ◽

Gerard Muyzer ◽

...

Keyword(s):

Electron Microscopy ◽

North Sea ◽

Dna Hybridization ◽

Aquatic Environments ◽

Virus Family ◽

The North ◽

The Family ◽

The North Sea ◽

Physiological Tests

ABSTRACT In recent years interest in bacteriophages in aquatic environments has increased. Electron microscopy studies have revealed high numbers of phage particles (104 to 107 particles per ml) in the marine environment. However, the ecological role of these bacteriophages is still unknown, and the role of the phages in the control of bacterioplankton by lysis and the potential for gene transfer are disputed. Even the basic questions of the genetic relationships of the phages and the diversity of phage-host systems in aquatic environments have not been answered. We investigated the diversity of 22 phage-host systems after 85 phages were collected at one station near a German island, Helgoland, located in the North Sea. The relationships among the phages were determined by electron microscopy, DNA-DNA hybridization, and host range studies. On the basis of morphology, 11 phages were assigned to the virus familyMyoviridae, 7 phages were assigned to the familySiphoviridae, and 4 phages were assigned to the familyPodoviridae. DNA-DNA hybridization confirmed that there was no DNA homology between phages belonging to different families. We found that the 22 marine bacteriophages belonged to 13 different species. The host bacteria were differentiated by morphological and physiological tests and by 16S ribosomal DNA sequencing. All of the bacteria were gram negative, facultatively anaerobic, motile, and coccoid. The 16S rRNA sequences of the bacteria exhibited high levels of similarity (98 to 99%) with the sequences of organisms belonging to the genus Pseudoalteromonas, which belongs to the γ subdivision of the class Proteobacteria.

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