PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

Floden, Evan; Chatzou, Maria; Magis, Cedrik; Notredame, Cédric; Chang, Jia‐Ming

doi:10.1093/nar/gkw300

Cited by 55 publications

(35 citation statements)

References 21 publications

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“…The amino acid sequences of this gene from the different species and the homologous C-terminal portion of the third VIPER gene were aligned using PSI-Coffee (Floden et al 2016) (). Visually, we divided the alignment into three regions that we designated I, II, and III (see Fig.…”

mentioning

confidence: 99%

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

Ludwig

Krieger

2016

Mem. Inst. Oswaldo Cruz

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Transposable elements are important residents of eukaryotic genomes and eventually the host can domesticate them to serve cellular functions. We reported here a possible domestication event of the vestigial interposed retroelement (VIPER) in trypanosomatids. We found a large gene in a syntenic location in Leishmania braziliensis, L. panamensis, Leptomanas pyrrhocoris, and Crithidia fasciculata whose products share similarity in the C-terminal portion with the third protein of VIPER. No remnants of other VIPER regions surrounding the gene sequence were found. We hypothesise that the domestication event occurred more than 50 mya and the conservation of this gene suggests it might perform some function in the host species.

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confidence: 99%

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

Ludwig

Krieger

2016

Mem. Inst. Oswaldo Cruz

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“…The collected ST sequences were aligned using TM-Coffee [82], a transmembrane protein alignment tool.…”

Section: Phylogenetic Analysis Of Stsmentioning

confidence: 99%

CAZyome and Sugar Transportome Unveil Singular Aspects of the Lignocellulolytic Enzyme System of Penicillium echinulatum 2HH

Lenz

Balbinot

Oliveira

et al. 2020

Preprint

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Background: The production of bioethanol using lignocellulosic feedstocks has proved to be a cutting-edge technology. However, this technology faces limitations such as cost and yield of enzymatic systems, required to degrade efficiently the polysaccharides of plant cell walls. Penicillium echinulatum 2HH is a widely studied ascomycete, known by its efficient cellulolytic cocktails. One strategy to improve the saccharification yields for commercial exploitation is the design of hypersecreting strains. However, molecular knowledge about the lignocellulolytic system of this specific fungus is scarce. Understanding both lignocellulolytic and sugar uptake systems is essential to obtain industrial strains with adequate efficiency for bioethanol production. Results: We report a comprehensive in silico characterization of CAZymes and sugar transporters of P. echinulatum 2HH. The CAZyome reveals an outstanding repertoire of enzymes involved in plant biomass degradation. Among them, we highlight the cellulolytic enzyme system whose genes are predominantly orthologous to P. oxalicum 114-2, demonstrating the high similarity of these phylogenetically related enzyme producers. We also report a LPMO-type enzyme of the AA16 family described for the first time in these fungi. In addition to the well-known high activity of ß-glucosidases, we found that coding genes for the AA16, GH5-4 and GH45 families comprehend the main differences in the cellulolytic complexes of P. echinulatum 2HH and P. oxalicum 114-2, when both are compared to commercial producers. Our phylogenetic analysis of the sugar transportome suggests that P. echinulatum 2HH diversity and specificity of STs include eight major families with specificity to different groups of sugars. Finally, our phylogenetic analyses enabled the identification of several iBGLs and STs potentially involved in the accumulation of intracellular cellodextrins.Conclusions: Overall, both CAZyome and sugar transportome of P. echinulatum revealed new insights into the mechanisms underlying a flexible and highly functional metabolism to degrade plant biomass. Peculiarities found in our study help to highlight the cellulolytic complex of P. echinulatum 2HH, contributing to the commercial ascendance of Penicillium spp. as cellulolytic enzyme producers. Furthermore, the first phylogenetic classification of STs and iBGLs shed new light into the role of these genes regarding the preferred carbon source during fungal growth. Along these lines, these iBGLs and STs comprise valuable gene targets to understand the regulatory mechanisms underlying cellulolytic enzymes and to design hypersecreting strains with adequate efficiency for bioethanol production in large-scale.

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“…Second, we compared the prediction of a single program (TM-Coffee [67]) on several homologs ("horizontal" approach). The corresponding alignment in text format is provided in S5 Alignment.…”

Section: Prediction Of Protein Structural Featuresmentioning

confidence: 99%

Parvovirus B19 and Human Parvovirus 4 Encode a Homologous "X Protein" in a Reading Frame Overlapping the VP1 Capsid Gene

Karlin¹

2020

Preprint

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30 years ago, researchers noticed that the capsid (VP1) gene of B19 parvovirus might encode a second protein, called "X", in an overlapping reading frame. Since then, experimental approaches failed to detect it. In contrast, sequence analyses can reliably predict whether a protein is expressed from an overlapping frame, provided that it is beneficial to the virus and thus under selection pressure. We used a dedicated software, Synplot2, to identify regions of VP1 likely to encode functional proteins in overlapping frames. Synplot2 detected the X open reading frame and confirmed it is under highly significant selection pressure. We discovered that the X protein is homologous to the ARF1 protein of human parvovirus 4, another suspected protein encoded in a frame overlapping VP1. These findings provide compelling evidence that the X protein must be expressed and functional. We predict that it contains a predicted transmembrane region. We found that the X frame contains a potential AUG start codon in parvovirus B19 and in all related species. Yet no currently known viral transcript has the potential to encode the X protein in a monocistronic fashion. Therefore, the X protein is probably expressed either from an unmapped monocistronic mRNA, or translated by a non-canonical mechanism from the VP1 mRNA or from a short transcript, R3, which has no currently known function. Finally, Synplot2 also detected proteins likely to be expressed from a frame overlapping VP1 in species distantly related to parvovirus B19: porcine parvovirus 2 and bovine parvovirus 3.

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PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

Cited by 55 publications

References 21 publications

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

CAZyome and Sugar Transportome Unveil Singular Aspects of the Lignocellulolytic Enzyme System of Penicillium echinulatum 2HH

Parvovirus B19 and Human Parvovirus 4 Encode a Homologous "X Protein" in a Reading Frame Overlapping the VP1 Capsid Gene

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