scholarly journals Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer

2020 ◽  
Vol 21 (S12) ◽  
Author(s):  
Maria A. Daugavet ◽  
Sergey V. Shabelnikov ◽  
Olga I. Podgornaya
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Amino Acid Sequence ◽  
Recombination Site

scholarly journals Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Roman Kogay ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nutrient Availability ◽  
Energy Cost ◽  
Group Selection ◽  
Protein Production ◽  
Bacterial Populations ◽  
Selection For ◽  
Transfer Agents

ABSTRACT Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria. The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells. IMPORTANCE Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria.

scholarly journals Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael J. Ormsby ◽  
Robert L. Davies
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Atlantic Salmon ◽  
Sequence Variation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Yersinia Ruckeri ◽  
Amino Acid Sequence Variation

AbstractYersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.

scholarly journals A Conserved Metal Binding Motif in the Bacillus subtilis Competence Protein ComFA Enhances Transformation

2017 ◽  
Vol 199 (15) ◽  
Author(s):  
Scott S. Chilton ◽  
Tanya G. Falbel ◽  
Susan Hromada ◽  
Briana M. Burton
Keyword(s):  
Bacillus Subtilis ◽  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Metal Binding ◽  
Dna Uptake ◽  
Content Type ◽  
Efficient Transformation ◽  
Dead Box ◽  
The Dead

ABSTRACT Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis. It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD box family of helicases/translocases. Here, we made a series of mutants to analyze conserved amino acid motifs in several regions of B. subtilis ComFA. First, we confirmed that ComFA activity requires amino acid residues conserved among the DEAD box helicases, and second, we show that a zinc finger-like motif consisting of four cysteines is required for efficient transformation. Each cysteine in the motif is important, and mutation of at least two of the cysteines dramatically reduces transformation efficiency. Further, combining multiple cysteine mutations with the helicase mutations shows an additive phenotype. Our results suggest that the helicase and metal binding functions are two distinct activities important for ComFA function during transformation. IMPORTANCE ComFA is a highly conserved protein that has a role in DNA uptake during natural competence, a mechanism for horizontal gene transfer observed in many bacteria. Investigation of the details of the DNA uptake mechanism is important for understanding the ways in which bacteria gain new traits from their environment, such as drug resistance. To dissect the role of ComFA in the DNA uptake machinery, we introduced point mutations into several motifs in the protein sequence. We demonstrate that several amino acid motifs conserved among ComFA proteins are important for efficient transformation. This report is the first to demonstrate the functional requirement of an amino-terminal cysteine motif in ComFA.

scholarly journals Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

2016 ◽  
Vol 7 ◽  
Author(s):  
Miguel A. Naranjo-Ortíz ◽  
Matthias Brock ◽  
Sascha Brunke ◽  
Bernhard Hube ◽  
Marina Marcet-Houben ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Metabolism Enzymes

scholarly journals A Tiling Algorithm-Based String Similarity Measure

2021 ◽  
Vol 9 ◽  
pp. 109-112
Author(s):  
Peter Z. Revesz
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Similarity Measure ◽  
Amino Acid Sequences ◽  
String Similarity

This paper describes a similarity measure for strings based on a tiling algorithm. The algorithm is applied to a pair of proteins that are described by their respective amino acid sequences. The paper also describes how the algorithm can be used to find highly conserved amino acid sequences and examples of horizontal gene transfer between different species

scholarly journals Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents

2020 ◽  
Author(s):  
Roman Kogay ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nutrient Availability ◽  
Energy Cost ◽  
Group Selection ◽  
Protein Production ◽  
Bacterial Populations ◽  
Selection For ◽  
Transfer Agents

AbstractGene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria. The GTAs can be induced under nutritional stress, incorporate random fragments of bacterial DNA into mini-phage particles, lyse the host cells and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that the GTA genes evolve under pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases when viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs are bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTA facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increase of nutrient availability resulting from the altruistic suicide of GTA-producing cells.ImportanceKin and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial Gene Transfer Agents (GTAs), but not related viruses, evolve under positive selection for the reduction of the energy cost of a GTA particle production. We hypothesize that GTAs are dedicated devices for the survival of bacteria under the conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and the increase of nutrient availability through the lysis of GTA-producing bacteria.

scholarly journals Enhancing FVIII Expression By Modifying B-Domain Sequence for Hemophilia A Gene Therapy

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3484-3484
Author(s):  
Doyoung Lee ◽  
Jenny McIntosh ◽  
Allison Dane ◽  
Cecilia Rosales ◽  
Anne Riddell ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Amino Acid ◽  
Gene Transfer ◽  
Amino Acid Sequence ◽  
Cell Lines ◽  
Hemophilia A ◽  
Amino Acid Content ◽  
Mrna Levels ◽  
Human Factor Viii ◽  
Equity Ownership

Abstract Background: We have previously shown that conserving six N-linked glycosylation sites of the human factor VIII (FVIII) B-domain sequences in a synthetic linker, V3 (31aa/N6), increased FVIII expression by 3-fold over B-domain deleted FVIII (BDD-FVIII) following AAV mediated gene transfer in mice (McIntosh et. al. Blood 2013). These N-linked glycosylation consensus sequences (N-X-T/S) are highly conserved across different species but their role in the context of transgenic FVIII expression following gene transfer remains unknown. We, therefore, undertook systemic B-domain linker engineering studies to elucidate the mechanism by which the V3-linker improves FVIII expression following AAV mediated gene transfer. Methods: A series of FVIII variants were made by modifying the B-domain linker size and amino acid sequence and then cloned into AAV or lentiviral vectors. The latter were used for making stable FVIII producer cell lines to facilitate biochemical characterization including glycome profile using MALDI-TOF mass spectrometry. The AAV vectors, in which expression of the FVIII gene was directed by a small synthetic liver specific promoter (HLP) were used to assess transgene expression in-vitro and in murine models. Results: Purified recombinant FVIII-V3 had the same biological activity as that of full-length and BDD FVIII protein concentrates when assessed by thrombin generation and vWF/FVIII binding affinity assays (Dissociation constant (KD) <1nM) suggesting that V3 linker did not interfere with the potency of FVIII. Replacement of the asparagine residues with alanine (FVIII-V5) within the six N-linked glycosylation motifs resulted in a >20 reduction in glycan structures but the expression profile and biological properties of FVIII-V5 were comparable to those of FVIII-V3. In contrast, FVIII-V1 (44aa), in which the N-linked glycosylation triplets in FVIII-V3 were flanked by two additional amino acids that are normally adjacent to these moieties in the native FVIII B-domain, was expressed at 3-fold low levels when compared to FVIII-V3 and V5 in mice. Similarly, randomly scrambling the amino acid sequence of the V3-linker (FVIII-V2) without modifying size resulted in a 7-fold decrease in FVIII expression levels in mice. Notably, FVIII-V3 and V5 mRNA levels were 4-fold higher than the levels observed with BDD-FVIII and FVIII-V1 variants. Deletion analysis of the V3 B-domain linker identified a shorter form (FVIII-N2 19aa/N2) that exhibited similar levels of FVIII secretion to those observed with FVIII-V3. Conclusion: We have critically evaluated the role of the FVIII B domain V3 linker on human FVIII expression in human cell lines and mice following AAV mediated gene transfer. In all cases, the FVIII-V3 variant performed better than the BDD-FVIII, in large part due to an increase in FVIII-V3 mRNA levels. Although the FVIII-V3 molecule is fully glycosylated, our studies show that glycan content did not significantly influence FVIII expression but increasing size and modifying amino-acid content of the linker, markedly reduced FVIII expression following AAV mediated gene transfer in mice. Therefore, the results presented here support the use of FVIII-V3 for gene therapy for hemophilia A in our on-going investigator lead Phase 1 trial. Disclosures McIntosh: Freeline: Consultancy, Equity Ownership; BioMarin: Patents & Royalties. Dane:Freeeline: Employment, Equity Ownership. Tuddenham:BioMarin: Consultancy, Patents & Royalties; Freeline: Consultancy. Nathwani:Freeline: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; BioMarin: Consultancy, Patents & Royalties; UniQure: Patents & Royalties.

Functional and phylogenetic analysis of a plant-inducible oligoribonuclease (orn) gene from an indigenous Pseudomonas plasmid

Microbiology ◽  
2004 ◽  
Vol 150 (9) ◽  
pp. 2889-2898 ◽  
Author(s):  
Xue-Xian Zhang ◽  
Andrew K. Lilley ◽  
Mark J. Bailey ◽  
Paul B. Rainey
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Gene Transfer ◽  
Amino Acid Sequence ◽  
Slow Growth ◽  
Single Gene ◽  
Transfer Event ◽  
Promoter Trapping ◽  
Inducible Genes

Application of a promoter-trapping strategy to identify plant-inducible genes carried on an indigenous Pseudomonas plasmid, pQBR103, revealed the presence of a putative oligoribonuclease (orn) gene that encodes a highly conserved 3′ to 5′ exoribonuclease specific for small oligoribonucleotides. The deduced amino acid sequence of the plasmid-derived orn (orn pl) showed three conserved motifs characteristic of Orn from both prokaryotes and eukaryotes. Deletion of orn pl generated no observable phenotype, but inactivation of the chromosomal copy caused slow growth in Pseudomonas putida KT2440. This defect was fully restored by complementation with orn from Escherichia coli (orn E.coli). Plasmid-derived orn pl was capable of partially complementing the P. putida orn mutant, demonstrating functionality of orn pl. Phylogenetic analysis showed that plasmid-encoded Orn was distinct from Orn encoded by the chromosome of proteobacteria. A survey of orn pl from related Pseudomonas plasmids showed a sporadic distribution but no sequence diversity. These data suggest that the orn pl was acquired by pQBR103 in a single gene-transfer event: the donor is unknown, but is unlikely to be a member of the Proteobacteria.

The staining pattern of the tropomyosin sequence is displayed in a new paracrystal

1986 ◽  
Vol 44 ◽  
pp. 150-151
Author(s):  
M.K. Lamvik ◽  
L.L. Klatt
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Staining Pattern ◽  
Banding Patterns ◽  
Mass Thickness ◽  
New Form

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.

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