scholarly journals Evolutionary convergence in lignin-degrading enzymes

2018 ◽  
Vol 115 (25) ◽  
pp. 6428-6433 ◽  
Author(s):  
Iván Ayuso-Fernández ◽  
Francisco J. Ruiz-Dueñas ◽  
Angel T. Martínez
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Acid Level ◽  
Lignin Degradation ◽  
Amino Acid Level ◽  
Surface Oxidation ◽  
Phenotypic Trait ◽  
Limiting Step ◽  
Powerful Strategy

The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.

scholarly journals Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese PeroxidaseIn Vitro

2019 ◽  
Vol 85 (13) ◽  
Author(s):  
Peter L. Herzog ◽  
Leander Sützl ◽  
Beate Eisenhut ◽  
Daniel Maresch ◽  
Dietmar Haltrich ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Lignin Degradation ◽  
Evolutionary Relationship ◽  
Physiological Role ◽  
Redox Cycling ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Pyranose Oxidase

ABSTRACTPyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacteriumKitasatospora aureofaciens(KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substratesin vitro. A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene fromK. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus,KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds betweenKaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity inKaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCEEstablishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase fromKitasatospora aureofaciensis of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively smallK. aureofaciensproteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.

scholarly journals Epidemiology and Genetic Variability of Circulating Influenza B Viruses in Uruguay, 2012–2019

2020 ◽  
Vol 8 (4) ◽  
pp. 591
Author(s):  
María José Rivas ◽  
Miguel Alegretti ◽  
Leticia Cóppola ◽  
Viviana Ramas ◽  
Héctor Chiparelli ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Human Population ◽  
Acid Level ◽  
Amino Acid Level ◽  
Respiratory Illness ◽  
Influenza B ◽  
Acute Respiratory Illness ◽  
Seasonal Epidemics ◽  
Almost All ◽  
Severe Acute Respiratory Illness

Influenza B viruses (IBV) are an important cause of morbidity and mortality during interpandemic periods in the human population. Two phylogenetically distinct IBV lineages, B/Yamagata and B/Victoria, co-circulate worldwide and they present challenges for vaccine strain selection. Until the present study, there was little information regarding the pattern of the circulating strains of IBV in Uruguay. A subset of positive influenza B samples from influenza-like illness (ILI) outpatients and severe acute respiratory illness (SARI) inpatients detected in sentinel hospitals in Uruguay during 2012–2019 were selected. The sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes showed substitutions at the amino acid level. Phylogenetic analysis reveals the co-circulation of both lineages in almost all seasonal epidemics in Uruguay, and allows recognizing a lineage-level vaccine mismatch in approximately one-third of the seasons studied. The epidemiological results show that the proportion of IBV found in ILI was significantly higher than the observed in SARI cases across different groups of age (9.7% ILI, 3.2% SARI) and patients between 5–14 years constituted the majority (33%) of all influenza B infection (p < 0.05). Interestingly, we found that individuals >25 years were particularly vulnerable to Yamagata lineage infections.

scholarly journals TT Virus Infection in Nonhuman Primates and Characterization of the Viral Genome: Identification of Simian TT Virus Isolates

2000 ◽  
Vol 74 (3) ◽  
pp. 1549-1553 ◽  
Author(s):  
Kenji Abe ◽  
Tomoko Inami ◽  
Koichi Ishikawa ◽  
Shin Nakamura ◽  
Shunji Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Nonhuman Primates ◽  
Amino Acid Level ◽  
Nucleotide Sequencing ◽  
Human Populations ◽  
Serum Samples ◽  
Tt Virus ◽  
Viral Genomes ◽  
Pcr Products

ABSTRACT Newly discovered TT virus (TTV) is widely distributed in human populations. To understand more about the relationship between TTV and its hosts, we tested 400 sera from various nonhuman primates for the presence of TTV DNA by PCR assay. We collected serum samples from 24 different species of nonhuman primates. TTV DNA was determined by PCR with primers designed from the 5′-end region of the TTV genome. Nucleotide sequencing and phylogenetic analysis of viral genomes were also performed. TTV DNA was detected in 87 of 98 (89%) chimpanzees and 3 of 21 (14%) crab-eating macaques. Nucleotide sequences of the PCR products obtained from both animals were 80 to 100% identical between two species. In contrast, the sequences differed from TTV isolates in humans by 24 to 33% at the nucleotide level and 36 to 50% at the amino acid level. Phylogenetic analysis demonstrated that all TTV isolates obtained from simians were distinct from the human TTV isolates. Furthermore, TTV in simians, but not in humans, was classified into three different genotypes. Our results indicate that TTV in simians represents a group different from, but closely related to, TTV in humans. From these results, we tentatively named this TTV simian TTV (s-TTV). The existence of the s-TTV will be important in determining the origin, nature, and transmission of human TTV and may provide useful animal models for studies of the infection and pathogenesis of this new DNA virus.

scholarly journals Characterization of Chelonus inanitus polydnavirus segments: sequences and analysis, excision site and demonstration of clustering

2002 ◽  
Vol 83 (1) ◽  
pp. 247-256 ◽  
Author(s):  
Stefan Wyder ◽  
Adrian Tschannen ◽  
Anita Hochuli ◽  
Andreas Gruber ◽  
Verena Saladin ◽  
...  
Keyword(s):  
Adult Development ◽  
Acid Level ◽  
Amino Acid Level ◽  
Inverted Repeats ◽  
Double Stranded Dna ◽  
Specific Time Point ◽  
Circular Molecule ◽  
Segmented Genome ◽  
Time Point

Polydnaviruses (genera Ichnovirus and Bracovirus) have a segmented genome of circular double-stranded DNA molecules, replicate in the ovary of parasitic wasps and are essential for successful parasitism of the host. Here we show the first detailed analysis of various segments of a bracovirus, the Chelonus inanitus virus (CiV). Four segments were sequenced and two of them, CiV12 and CiV14, were found to be closely related while CiV14.5 and CiV16.8 were unrelated. CiV12, CiV14.5 and CiV16.8 are unique while CiV14 occurs also nested in another larger segment. All four segments are predicted to contain genes and predictions could be substantiated in most cases. Comparison with databases revealed no significant similarities at either the nucleotide or amino acid level. Inverted repeats with identities between 77% and 92% and lengths between 26 bp and 100 bp were found on all segments outside of predicted genes. Hybridization experiments indicate that CiV12 and CiV14 are both flanked by other virus segments, suggesting that proviral CiV segments are clustered in the genome of the wasp. The integration/excision site of CiV14 was analysed and compared to that of CiV12. On both termini of proviral CiV12 and CiV14 as well as in the excised circular molecule and the rejoined DNA a very similar repeat of 14 bp was found. A model to illustrate where the terminal repeats might recombine to yield the circular molecule is presented. Excision of CiV12 and CiV14 is restricted to the female and sets in at a very specific time-point in pupal–adult development.

Morphological, histological and molecular characterization of Myxidium cf. rhodei infecting the kidney of Rutilus rutilus

2020 ◽  
Vol 141 ◽  
pp. 39-46
Author(s):  
MD Dorjievna Batueva ◽  
X Pan ◽  
J Zhang ◽  
X Liu ◽  
W Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rutilus Rutilus ◽  
Longitudinal Axis ◽  
Suture Line ◽  
Present Species ◽  
Supplementary Data

In the present study, we provide supplementary data for Myxidium cf. rhodei Léger, 1905 based on morphological, histological and molecular characterization. M. cf. rhodei was observed in the kidneys of 918 out of 942 (97%) roach Rutilus rutilus (Linnaeus, 1758). Myxospores of M. cf. rhodei were fusiform with pointed ends, measuring 12.7 ± 0.1 SD (11.8-13.4) µm in length and 4.6 ± 0.1 (3.8-5.4) µm in width. Two similar pear-shaped polar capsules were positioned at either ends of the longitudinal axis of the myxospore: each of these capsules measured 4.0 ± 0.1 (3.1-4.7) µm in length and 2.8 ± 0.1 (2.0-4.0) µm in width. Polar filaments were coiled into 4 to 5 turns. Approximately 18-20 longitudinal straight ridges were observed on the myxospore surface. The suture line was straight and distinctive, running near the middle of the valves. Histologically, the plasmodia of the present species were found in the Bowman’s capsules, and rarely in the interstitium of the host. Phylogenetic analysis revealed that M. cf. rhodei was sister to M. anatidum in the Myxidium clade including most Myxidium species from freshwater hosts.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

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