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 Comparison of Two Aquatic Alphaviruses, Salmon Pancreas Disease Virus and Sleeping Disease Virus, by Using Genome Sequence Analysis, Monoclonal Reactivity, and Cross-Infection

2002 ◽  
Vol 76 (12) ◽  
pp. 6155-6163 ◽  
Author(s):  
Jonathan Weston ◽  
Stéphane Villoing ◽  
Michel Brémont ◽  
Jeanette Castric ◽  
Martin Pfeffer ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Atlantic Salmon ◽  
Disease Virus ◽  
Antigenic Variation ◽  
Encephalitis Virus ◽  
Virus Species ◽  
Pancreas Disease ◽  
Equine Encephalitis Virus ◽  
Salmon Pancreas Disease Virus

ABSTRACT Cell culture isolates of salmon pancreas disease virus (SPDV) of farmed Atlantic salmon and sleeping disease virus (SDV) of rainbow trout were compared. Excluding the poly(A) tracts, the genomic nucleotide sequences of SPDV and SDV RNAs include 11,919 and 11,900 nucleotides, respectively. Phylogenetic analysis places SPDV and SDV between the New World viruses of Venezuelan equine encephalitis virus and Eastern equine encephalitis virus and the Old World viruses of Aura virus and Sindbis virus. When compared to each other, SPDV and SDV show 91.1% nucleotide sequence identity over their complete genomes, with 95 and 93.6% amino acid identities over their nonstructural and structural proteins, respectively. Notable differences between the two viruses include a 24-nucleotide insertion in the C terminus of nsP3 protein of SPDV and amino acid sequence variation at the C termini of the capsid and E1 proteins. Experimental infections of Atlantic salmon and rainbow trout with SPDV and SDV confirmed that the disease lesions induced by SPDV and SDV were similar in nature. Although infections with SPDV and SDV produced similar levels of histopathology in rainbow trout, SDV induced significantly less severe lesions in salmon than did SPDV. Virus neutralization tests performed with sera from experimentally infected salmon indicated that SPDV and SDV belonged to the same serotype; however, antigenic variation was detected among SDV and geographically different SPDV isolates by using monoclonal antibodies. Although SPDV and SDV exhibit minor biological differences, we conclude on the basis of the close genetic similarity that SPDV and SDV are closely related isolates of the same virus species for which the name Salmonid alphavirus is proposed.

scholarly journals Molecular Phylogeny of the Salmonellae: Relationships among Salmonella Species and Subspecies Determined from Four Housekeeping Genes and Evidence of Lateral Gene Transfer Events

2008 ◽  
Vol 190 (21) ◽  
pp. 7060-7067 ◽  
Author(s):  
J. R. McQuiston ◽  
S. Herrera-Leon ◽  
B. C. Wertheim ◽  
J. Doyle ◽  
P. I. Fields ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Salmonella Enterica ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Diverse Group ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Common Serotypes

ABSTRACT The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

scholarly journals Evolution and Molecular Phylogeny of Listeria monocytogenes Isolated from Human and Animal Listeriosis Cases and Foods

2005 ◽  
Vol 187 (16) ◽  
pp. 5537-5551 ◽  
Author(s):  
K. K. Nightingale ◽  
K. Windham ◽  
M. Wiedmann
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Positive Selection ◽  
New York State ◽  
Housekeeping Genes ◽  
Acid Sites ◽  
Food Samples ◽  
Phylogenetic Lineages

ABSTRACT To probe the evolution and phylogeny of Listeria monocytogenes from defined host species and environments, L. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in New York State between 1999 and 2001. Partial sequencing of four housekeeping genes (gap, prs, purM, and ribC), one stress response gene (sigB), and two virulence genes (actA and inlA) revealed between 11 (gap) and 33 (inlA) allelic types as well as 52 sequence types (unique combination of allelic types). actA, ribC, and purM demonstrated the highest levels of nucleotide diversity (π > 0.05). actA and inlA as well as prs and the hypervariable housekeeping genes ribC and purM showed evidence of horizontal gene transfer and recombination. actA and inlA also showed evidence of positive selection at specific amino acid sites. Maximum likelihood phylogenies for all seven genes confirmed that L. monocytogenes contains two deeply separated evolutionary lineages. Lineage I was found to be highly clonal, while lineage II showed greater diversity and evidence of horizontal gene transfer. Allelic types were exclusive to lineages, except for a single gap allele, and nucleotide distance within lineages was much lower than that between lineages, suggesting that genetic exchange between lineages is rare. Our data show that (i) L. monocytogenes is a highly diverse species with at least two distinct phylogenetic lineages differing in their evolutionary history and population structure and (ii) horizontal gene transfer as well as positive selection contributed to the evolution of L. monocytogenes.

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.

Characterization of a transcriptionally active Tc1-like transposon in the microsporidian Nosema bombycis

2010 ◽  
Vol 55 (1) ◽  
Author(s):  
Jinshan Xu ◽  
Jie Luo ◽  
Bettina Debrunner-Vossbrinck ◽  
Xiaoyan Zhang ◽  
Hangdeng Liu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Transposable Element ◽  
Transcriptional Activity ◽  
Sequence Variation ◽  
Biological Control Agents ◽  
Functional Motif ◽  
Nosema Bombycis ◽  
Amino Acid Sequence Variation ◽  
Unique Clade

AbstractThe Tc1 transposable element has been found in a wide variety of organisms including vertebrates, insects and fungi but has not been previously reported in Microsporidia. In this study we characterize an intact DNA transposon (NbTc1) from the microsporidian Nosema bombycis. This transposable element encodes a 337 amino acid transposase sequence, which contains the D,D34E functional motif required for transposition. A Southern blot of N. bombycis DNA separated by pulsedesis shows that copies of the NbTc1 transposon are present on 10 of the 14 chromosomes of N. bombycis. Amino acid sequence variation among copies of the NbTc1 is low, suggesting a conserved function for this transposon within N. bombycis. Phylogenetic analysis indicates that NbTc1 is a new member of the Tc1 family lineage, quite distinct from all previously described Tc1 elements, including those from fungi, indicating that NbTc1 forms a unique clade of the Tc1 superfamily. However, the Tc1 transposon is too divergent to resolve the major phylogenetic relationships among these superfamilies. Reverse transcriptase PCR and Solexa sequencing suggest that NbTc1 possesses transcriptional activity. Considering the interest in Microsporidia as biological control agents, the NbTc1 transposon may be a useful vector for the efficient transfection of these important parasites into host species.

scholarly journals Comparative susceptibility of Atlantic salmon and rainbow trout to Yersinia ruckeri: Relationship to O antigen serotype and resistance to serum killing

2011 ◽  
Vol 147 (1-2) ◽  
pp. 155-161 ◽  
Author(s):  
Sarah J. Haig ◽  
Robert L. Davies ◽  
Timothy J. Welch ◽  
R. Allan. Reese ◽  
David W. Verner-Jeffreys
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Yersinia Ruckeri ◽  
O Antigen ◽  
Serum Killing ◽  
Comparative Susceptibility

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.

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