Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: Possibility of horizontal gene transfer in purple bacteria

1993 ◽  
Vol 36 (3) ◽  
pp. 185-191 ◽  
Author(s):  
Kenji V. P. Nagashima ◽  
Keizo Shimada ◽  
Katsumi Matsuura
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Purple Bacteria ◽  
Photosynthetic Genes ◽  
Rhodocyclus Gelatinosus

scholarly journals Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Ahmed M. Moustafa ◽  
Senthil Kumar Velusamy ◽  
Lidiya Denu ◽  
Apurva Narechania ◽  
Daniel H. Fine ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Strong Association ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Short Chain ◽  
Oral Microbiota ◽  
Content Type ◽  
History Of ◽  
The Impact

ABSTRACT Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease. IMPORTANCE There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. We propose that SCFAs allow Aggregatibacter actinomycetemcomitans (Aa) to adapt to the subgingival anaerobic environment, which is the site of human periodontitis. Under anaerobic, SCFA-rich conditions, human-derived Aa strains that possess butyrate metabolism genes form strong biofilms and upregulate virulence genes. Our phylogenetic analysis highlights a long history of evolution of Aa with its primate hosts and suggests that the acquisition of butyrate metabolism genes may have been a critical step in allowing Aa to colonize a new niche and cause disease in humans. Overall, this study highlights the important role that horizontal gene transfer may play in microbial adaptation and the evolution of infectious disease.

scholarly journals Phylogenetic analysis of genomic islands in closely-related species belonging to Sinorhizobium sp.

2020 ◽  
Author(s):  
M. E. Vladimirova ◽  
V. S. Muntyan ◽  
A. S. Saksaganskaya ◽  
B. V. Simarov ◽  
M. L. Roumiantseva
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Related Species ◽  
Genomic Islands ◽  
Closely Related Species ◽  
Homologous Sequences

Genomic islands of closely related S. meliloti and S. medicae species were evaluated and homologous sequences were identified; it has been suggested that horizontal gene transfer occurs at homologous tRNA sites.

scholarly journals A comprehensive phylogenetic analysis of the serpin superfamily

2020 ◽  
Author(s):  
Matthew A. Spence ◽  
Matthew D. Mortimer ◽  
Ashley M. Buckle ◽  
Bui Quang Minh ◽  
Colin J. Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

scholarly journals Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes

2020 ◽  
Author(s):  
Zhengmi He ◽  
Pan Long ◽  
Fang Fang ◽  
Sainan Li ◽  
Ping Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
North America ◽  
Horizontal Gene Transfer ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Taxonomic Status ◽  
Chemical Substance ◽  
Prolyl Oligopeptidase ◽  
Pcr Cloning

Abstract Background Amanitin-producing mushrooms, mainly distributed in the genera Amanita , Galerina and Lepiota , possess MSDIN gene family for the biosynthesis of many cyclopeptides catalyzed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be a efficient way to mine MSDIN and POP genes in these lethal mushrooms. Until now, only A . palloides and A. bisporigera from North America and A . exitialis from Asia have been studied based on transcriptome analysis. However, MSDIN and POP genes of many amanitin-producing mushrooms in China remain unstudied, and hence the transcriptomes of these speices deserve to be analysed. Results In this study, the MSDIN and POP genes from ten Amanita species, two Galerina species and Lepiota venenata were studied and the phylogenetic relationships of their MSDIN and POP genes were analyzed. Through transcriptome sequencing and PCR cloning, 19 POP genes and 151 MSDIN genes predicted to encode 98 non-duplicated cyclopeptides, including α-amanitin, β-amanitin, phallacidin, phalloidin and 94 unknown peptides, were found in these species. Phylogenetic analysis showed that toxin peptide genes were clustered depending on the chemical substance within genus while depending on the taxonomy between genus and that the POPA genes of Amanita , Galerina and Lepiota were clustered and separated in three different groups, but the POPB genes of the three distinct genera were clustered in a highly monophyletic group. Conclusions These results above indicate that lethal Amanita species have the genetic capacity to produce numerous cyclopeptides, most of which are unknown, while lethal Galerina and Lepiota species seem to only have the genetic capacity to produce α-amanitin. Additionally, the POPB phylogeny of Amanita , Galerina and Lepiota conflicts with the taxonomic status of the three genera, suggesting that horizontal gene transfer might occur among the three genera.

scholarly journals Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes

2020 ◽  
Author(s):  
Zhengmi He ◽  
Pan Long ◽  
Fang Fang ◽  
Sainan Li ◽  
Ping Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
North America ◽  
Horizontal Gene Transfer ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Taxonomic Status ◽  
Chemical Substance ◽  
Prolyl Oligopeptidase ◽  
Pcr Cloning

Abstract Background: Amanitin-producing mushrooms, mainly distributed in the genera Amanita , Galerina and Lepiota , possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be an efficient way to mine MSDIN and POP genes in these lethal mushrooms. Thus far, only A . palloides and A. bisporigera from North America and A . exitialis and A. rimosa from Asia have been studied based on transcriptome analysis. However, the MSDIN and POP genes of many amanitin-producing mushrooms in China remain unstudied; hence, the transcriptomes of these speices deserve to be analysed. Results: In this study, the MSDIN and POP genes from ten Amanita species, two Galerina species and Lepiota venenata were studied and the phylogenetic relationships of their MSDIN and POP genes were analysed. Through transcriptome sequencing and PCR cloning, 19 POP genes and 151 MSDIN gened to encode 98 non-duplicated cyclopeptides, including α- amanitin, β-amanitin, phallacidin, phalloidin and 94 unknown peptides, were found in these species. Phylogenetic analysis showed that (1) MSDIN genes generally clustered depending on the taxonomy of the genus, while Amanita MSDIN genes clustered depending on the chemical substance; and (2) the POPA genes of Amanita , Galerina and Lepiota clustered and were separated into three different groups, but the POPB genes of the three distinct genera were clustered in a highly supported monophyletic group. Conclusions: These results indicate that lethal Amanita species have the genetic capacity to produce numerous cyclopeptides, most of which are unknown, while lethal Galerina and Lepiota species seem to only have the genetic capacity to produce α-amanitin. Additionally, the POPB phylogeny of Amanita , Galerina and Lepiota conflicts with the taxonomic status of the three genera, suggesting that underlying horizontal gene transfer has occurred among these three genera.

scholarly journals Horizontal transfer in bacterial Methionyl tRNA synthetase is very common shown by Genus and phyla level phylogenetic analysis.

2016 ◽  
Author(s):  
Prabhakar Ghorpade ◽  
Avinash Pange ◽  
Bhaskar Sharma
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Single Copy ◽  
Trna Synthetase ◽  
Species Tree ◽  
Large Trees ◽  
Conserved Gene ◽  
Methionyl Trna Synthetase ◽  
Informational Gene

Methionyl tRNA synthetase is single copy informational gene in Salmonella typhimurium. Informational genes are more conserved than operational genes. In this study we had analyzed HGT events within MetG sequences of different bacterial genera. A species tree based on 16srRNA sequences of the same genus was drawn evaluated against the generally accepted species tree of the bacteria. MetG phylogenetic tree was evaluated against the 16srRNAS tree and HGT event identified. Similarly phyla trees were made and HGT event identified. 24 HGT events were identified between genus and 11 within phyla. MetG is a considered as conserved gene finding so many HGT event in this gene indicate that horizontal gene transfer is very common in this gene. Manual tree making for phyla could help to understand phylogenetic relationships between very large trees.

scholarly journals A Comprehensive Phylogenetic Analysis of the Serpin Superfamily

2021 ◽  
Author(s):  
Matthew A Spence ◽  
Matthew D Mortimer ◽  
Ashley M Buckle ◽  
Bui Quang Minh ◽  
Colin J Jackson
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Convergent Evolution ◽  
Alternative Hypothesis ◽  
Structural Alignment ◽  
High Homology ◽  
Physiological Processes ◽  
New Directions ◽  
Hub Proteins

Abstract Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

scholarly journals Structure and Evolution of the hAT Transposon Superfamily

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 949-957 ◽  
Author(s):  
Eitan Rubin ◽  
Gila Lithwick ◽  
Avraham A Levy
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Inverted Repeats ◽  
Mobile Dna ◽  
Terminal Inverted Repeats ◽  
The Public ◽  
Hat Superfamily ◽  
Plant Fungi ◽  
Sequence Databases

Abstract The maize transposon Activator (Ac) was the first mobile DNA element to be discovered. Since then, other elements were found that share similarity to Ac, suggesting that it belongs to a transposon superfamily named hAT after hobo from Drosophila, Ac from maize, and Tam3 from snapdragon. We addressed the structure and evolution of hAT elements by developing new tools for transposon mining and searching the public sequence databases for the hallmarks of hAT elements, namely the transposase and short terminal inverted repeats (TIRs) flanked by 8-bp host duplications. We found 147 hAT-related sequences in plants, animals, and fungi. Six conserved blocks could be identified in the transposase of most hAT elements. A total of 41 hAT sequences were flanked by TIRs and 8-bp host duplications and, out of these, 34 sequences had TIRs similar to the consensus determined in this work, suggesting that they are active or recently active transposons. Phylogenetic analysis and clustering of hAT sequences suggest that the hAT superfamily is very ancient, probably predating the plant-fungi-animal separation, and that, unlike previously proposed, there is no evidence that horizontal gene transfer was involved in the evolution of hAT elements.

scholarly journals Characterization of a Novel Megabirnavirus from Sclerotinia sclerotiorum Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus

2015 ◽  
Vol 89 (16) ◽  
pp. 8567-8579 ◽  
Author(s):  
Minghong Wang ◽  
Yong Wang ◽  
Xiangzhong Sun ◽  
Jiasen Cheng ◽  
Yanping Fu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Sclerotinia Sclerotiorum ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Protease Domain ◽  
Content Type ◽  
Ssrna Virus ◽  
L1 And L2

ABSTRACTMycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus,Sclerotiniasclerotiorummegabirnavirus1(SsMBV1), in an apparently hypovirulent strain (SX466) ofSclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related toRosellinia necatrixmegabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5′-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) ofCryphonectriahypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1.IMPORTANCEMycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized a novel dsRNA virus (Sclerotinia sclerotiorummegabirnavirus 1 [SsMBV1]) that was isolated from an apparently hypovirulent strain, SX466, ofSclerotinia sclerotiorum. Although SsMBV1 is phylogenetically related to RnMBV1, SsMBV1 is markedly distinct from other reported megabirnaviruses with two features of VLPs and conserved domains. Our results convincingly showed that SsMBV1 is viable in the absence of L2-dsRNA/SsMBV1 (a potential large satellite-like RNA or genuine genomic virus component). More interestingly, we detected a conserved papain-like protease domain that commonly exists in ssRNA viruses, including members of the familiesPotyviridaeandHypoviridae. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer might have occurred from an ssRNA virus to a dsRNA virus, which may provide new insights into the evolutionary history of dsRNA and ssRNA viruses.

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