2022
|
Maciszewski, Kacper; Dabbagh, Nadja; Preisfeld, Angelika; Karnkowska, Anna Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes Journal Article Molecular Phylogenetics and Evolution, 170 , pp. 107441, 2022, ISSN: 1055-7903. Abstract | Links | BibTeX @article{MACISZEWSKI2022107441,
title = {Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes},
author = {Kacper Maciszewski and Nadja Dabbagh and Angelika Preisfeld and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S1055790322000549},
doi = {https://doi.org/10.1016/j.ympev.2022.107441},
issn = {1055-7903},
year = {2022},
date = {2022-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {170},
pages = {107441},
abstract = {Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity and history of maturases, an essential gene family among euglenophytes, we searched for their homologs in newly sequenced and published plastid genomes representing all major euglenophyte lineages. We found that maturase content in plastid genomes has a patchy distribution, with a maximum of eight of them present in Eutreptiella eupharyngea. The most basal lineages of euglenophytes, Eutreptiales, share the highest number of maturases, but the lowest number of introns. We also identified a peculiar convoluted structure of a gene located in an intron, in a gene within an intron, within yet another gene, present in some Eutreptiales. Further investigation of functional domains of identified maturases show that most of them lost at least one of the functional domains, which implies that the patchy maturase distribution is due to frequent inactivation and eventual loss over time. Finally, we identified the diversified evolutionary origin of analysed maturases, which were acquired along with the green algal plastid or horizontally transferred. These findings indicate that euglenophytes' plastid maturases have experienced a surprisingly dynamic history due to gains from diversified donors, their retention, and loss.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity and history of maturases, an essential gene family among euglenophytes, we searched for their homologs in newly sequenced and published plastid genomes representing all major euglenophyte lineages. We found that maturase content in plastid genomes has a patchy distribution, with a maximum of eight of them present in Eutreptiella eupharyngea. The most basal lineages of euglenophytes, Eutreptiales, share the highest number of maturases, but the lowest number of introns. We also identified a peculiar convoluted structure of a gene located in an intron, in a gene within an intron, within yet another gene, present in some Eutreptiales. Further investigation of functional domains of identified maturases show that most of them lost at least one of the functional domains, which implies that the patchy maturase distribution is due to frequent inactivation and eventual loss over time. Finally, we identified the diversified evolutionary origin of analysed maturases, which were acquired along with the green algal plastid or horizontally transferred. These findings indicate that euglenophytes' plastid maturases have experienced a surprisingly dynamic history due to gains from diversified donors, their retention, and loss. |
2021
|
Kostygov, Alexei Y; Karnkowska, Anna; Votypka, Jan; Tashyreva, Daria; Maciszewski, Kacper; Yurchenko, Vyacheslav; Lukes, Julius Euglenozoa : taxonomy, diversity and ecology, symbioses and viruses Journal Article Open Biology, 11 (3), pp. 200407-200407, 2021, ISBN: 0000000337. Abstract | Links | BibTeX @article{Kostygov2021,
title = {Euglenozoa : taxonomy, diversity and ecology, symbioses and viruses},
author = {Alexei Y Kostygov and Anna Karnkowska and Jan Votypka and Daria Tashyreva and Kacper Maciszewski and Vyacheslav Yurchenko and Julius Lukes},
url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.200407},
doi = {https://doi.org/10.1098/rsob.200407},
isbn = {0000000337},
year = {2021},
date = {2021-01-01},
journal = {Open Biology},
volume = {11},
number = {3},
pages = {200407-200407},
abstract = {Euglenozoa is a species-rich group of protists, which have extremely diverse
lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids,
mostly free-living diplonemids, heterotrophic and photosynthetic euglenids,
as well as deep-sea symbiontids. Although they form a well-supported
monophyletic group, these morphologically rather distinct groups are
almost never treated together in a comparative manner, as attempted here.
We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of
euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is
known about viruses infecting euglenozoans, as well as their relationships
with ecto- and endosymbiotic bacteria.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenozoa is a species-rich group of protists, which have extremely diverse
lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids,
mostly free-living diplonemids, heterotrophic and photosynthetic euglenids,
as well as deep-sea symbiontids. Although they form a well-supported
monophyletic group, these morphologically rather distinct groups are
almost never treated together in a comparative manner, as attempted here.
We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of
euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is
known about viruses infecting euglenozoans, as well as their relationships
with ecto- and endosymbiotic bacteria. |
2020
|
Kayama, Motoki; Maciszewski, Kacper; Yabuki, Akinori; Miyashita, Hideaki; Karnkowska, Anna; Kamikawa, Ryoma Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis. Journal Article Frontiers in Plant Science, 11 , pp. 1859 , 2020. Links | BibTeX @article{Kayama2020,
title = {Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis.},
author = {Motoki Kayama and Kacper Maciszewski and Akinori Yabuki and Hideaki Miyashita and Anna Karnkowska and Ryoma Kamikawa },
url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.602455/full},
doi = {https://doi.org/10.3389/fpls.2020.602455},
year = {2020},
date = {2020-11-27},
journal = {Frontiers in Plant Science},
volume = {11},
pages = {1859 },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Bakuła, Zofia; Gromadka, Robert; Gawor, Jan; Siedlecki, Paweł; Pomorski, Jan J; Maciszewski, Kacper; Gromadka, Agnieszka; Karnkowska, Anna; Jagielski, Tomasz Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii Journal Article Frontiers in Plant Science, 11 , pp. 1296, 2020. Links | BibTeX @article{10.3389/fpls.2020.01296,
title = {Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii},
author = {Zofia Bakuła and Robert Gromadka and Jan Gawor and Paweł Siedlecki and Jan J. Pomorski and Kacper Maciszewski and Agnieszka Gromadka and Anna Karnkowska and Tomasz Jagielski},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.01296/full},
doi = {10.3389/fpls.2020.01296},
year = {2020},
date = {2020-09-01},
journal = {Frontiers in Plant Science},
volume = {11},
pages = {1296},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2019
|
Maciszewski, Kacper; Karnkowska, Anna Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles Journal Article Current Opinion in Genetics & Development, 58-59 , pp. 33-39, 2019, ISSN: 0959-437X, (Evolutionary genetics). Abstract | Links | BibTeX @article{MACISZEWSKI201933,
title = {Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles},
author = {Kacper Maciszewski and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S0959437X19300425},
doi = {https://doi.org/10.1016/j.gde.2019.07.013},
issn = {0959-437X},
year = {2019},
date = {2019-01-01},
journal = {Current Opinion in Genetics & Development},
volume = {58-59},
pages = {33-39},
abstract = {Our knowledge on the variability of the reduced forms of endosymbiotic organelles – mitochondria and plastids – is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles’ diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles’ eventual fate, and a proposed classification of nonphotosynthetic plastids.},
note = {Evolutionary genetics},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Our knowledge on the variability of the reduced forms of endosymbiotic organelles – mitochondria and plastids – is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles’ diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles’ eventual fate, and a proposed classification of nonphotosynthetic plastids. |
Han, Kwi Young; Maciszewski, Kacper; Graf, Louis; Yang, Ji Hyun; Andersen, Robert A; Karnkowska, Anna; Yoon, Hwan Su Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization Journal Article Journal of Phycology, 55 (5), pp. 1166-1180, 2019. Abstract | Links | BibTeX @article{https://doi.org/10.1111/jpy.12904,
title = {Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization},
author = {Kwi Young Han and Kacper Maciszewski and Louis Graf and Ji Hyun Yang and Robert A Andersen and Anna Karnkowska and Hwan Su Yoon},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12904},
doi = {https://doi.org/10.1111/jpy.12904},
year = {2019},
date = {2019-01-01},
journal = {Journal of Phycology},
volume = {55},
number = {5},
pages = {1166-1180},
abstract = {Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation. |
Jagielski, Tomasz; Bakuła, Zofia; Gawor, Jan; Maciszewski, Kacper; Kusber, Wolf-Henning; Dyląg, Mariusz; Nowakowska, Julita; Gromadka, Robert; Karnkowska, Anna The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies Journal Article Algal Research, 43 , pp. 101639, 2019, ISSN: 2211-9264. Abstract | Links | BibTeX @article{JAGIELSKI2019101639,
title = {The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies},
author = {Tomasz Jagielski and Zofia Bakuła and Jan Gawor and Kacper Maciszewski and Wolf-Henning Kusber and Mariusz Dyląg and Julita Nowakowska and Robert Gromadka and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S2211926419303509},
doi = {https://doi.org/10.1016/j.algal.2019.101639},
issn = {2211-9264},
year = {2019},
date = {2019-01-01},
journal = {Algal Research},
volume = {43},
pages = {101639},
abstract = {The only algae which are able to inflict disease on humans and other mammals through active invasion and spread within the host tissues belong to either of two genera: Chlorella and Prototheca. Whereas Chlorella infections are extremely rare, with only two human cases reported in the literature, protothecosis is an emerging disease of humans and domestic animals, especially dairy cows. The genus Prototheca, erected by Krüger in 1894, has undergone several significant revisions, as more phenotypic, chemotaxonomic, and molecular data have become available. Due to this, a large number of Prototheca strains have been accumulated in public culture collections, over the years, where they still exist under outdated or invalid infraspecific or species names. In this study, the partial cytb gene was used as a marker to revise the taxonomy and nomenclature of a set of Prototheca strains, preserved in major algae culture repositories worldwide. Within the genus, two main lineages were observed, with a dominance of typically dairy cattle-associated (i.e. P. ciferrii, formerly P. zopfii gen. 1, the here validated P. blaschkeae, and one newly erected species, namely P. bovis, formerly P. zopfii gen. 2) and human-associated (i.e. P. wickerhamii, P. cutis, P. miyajii) species, respectively. In the former lineage, three newly described species were allocated, namely P. cookei sp. nov., P. cerasi sp. nov., and P. pringsheimii sp. nov., and the lecto- and epitypified P. zopfii species. The second, or so-called P. wickerhamii lineage, incorporated a newly proposed species of P. xanthoriae sp. nov. These protothecans were shown as the closest relatives of the photosynthetic genera, Chlorella and Auxenochlorella. The environmental species P. ulmea was synonymized with the lecto- and epitypified P. moriformis species. For circumscription and differentiation of Prototheca spp., the use of phenotypic characters, and morphology in particular, is of limited value and should rather be auxiliary to molecular marker-based approaches. As demonstrated in our previous study and corroborated in the present one, the cytb gene provides higher resolution than the conventional rDNA markers, and currently represents the most efficient barcode for the Prototheca algae.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The only algae which are able to inflict disease on humans and other mammals through active invasion and spread within the host tissues belong to either of two genera: Chlorella and Prototheca. Whereas Chlorella infections are extremely rare, with only two human cases reported in the literature, protothecosis is an emerging disease of humans and domestic animals, especially dairy cows. The genus Prototheca, erected by Krüger in 1894, has undergone several significant revisions, as more phenotypic, chemotaxonomic, and molecular data have become available. Due to this, a large number of Prototheca strains have been accumulated in public culture collections, over the years, where they still exist under outdated or invalid infraspecific or species names. In this study, the partial cytb gene was used as a marker to revise the taxonomy and nomenclature of a set of Prototheca strains, preserved in major algae culture repositories worldwide. Within the genus, two main lineages were observed, with a dominance of typically dairy cattle-associated (i.e. P. ciferrii, formerly P. zopfii gen. 1, the here validated P. blaschkeae, and one newly erected species, namely P. bovis, formerly P. zopfii gen. 2) and human-associated (i.e. P. wickerhamii, P. cutis, P. miyajii) species, respectively. In the former lineage, three newly described species were allocated, namely P. cookei sp. nov., P. cerasi sp. nov., and P. pringsheimii sp. nov., and the lecto- and epitypified P. zopfii species. The second, or so-called P. wickerhamii lineage, incorporated a newly proposed species of P. xanthoriae sp. nov. These protothecans were shown as the closest relatives of the photosynthetic genera, Chlorella and Auxenochlorella. The environmental species P. ulmea was synonymized with the lecto- and epitypified P. moriformis species. For circumscription and differentiation of Prototheca spp., the use of phenotypic characters, and morphology in particular, is of limited value and should rather be auxiliary to molecular marker-based approaches. As demonstrated in our previous study and corroborated in the present one, the cytb gene provides higher resolution than the conventional rDNA markers, and currently represents the most efficient barcode for the Prototheca algae. |
2018
|
Jagielski, Tomasz; Gawor, Jan; Bakuła, Zofia; Decewicz, Przemysław; Maciszewski, Kacper; Karnkowska, Anna cytb as a New Genetic Marker for Differentiation of Prototheca Species Journal Article Journal of Clinical Microbiology, 56 (10), 2018, ISSN: 0095-1137. Abstract | Links | BibTeX @article{Jagielskie00584-18,
title = {cytb as a New Genetic Marker for Differentiation of Prototheca Species},
author = {Tomasz Jagielski and Jan Gawor and Zofia Bakuła and Przemysław Decewicz and Kacper Maciszewski and Anna Karnkowska},
editor = {Brad Fenwick},
url = {https://jcm.asm.org/content/56/10/e00584-18},
doi = {10.1128/JCM.00584-18},
issn = {0095-1137},
year = {2018},
date = {2018-01-01},
journal = {Journal of Clinical Microbiology},
volume = {56},
number = {10},
publisher = {American Society for Microbiology Journals},
abstract = {Achlorophyllous unicellular microalgae of the genus Prototheca (Trebouxiophyceae, Chlorophyta) are the only known plants that cause infections in both humans and animals, collectively referred to as protothecosis. Human protothecosis, most commonly manifested as cutaneous, articular, and disseminated disease, is primarily caused by Prototheca wickerhamii, followed by Prototheca zopfii and, sporadically, by Prototheca cutis and Prototheca miyajii. In veterinary medicine, however, P. zopfii is a major pathogen responsible for bovine mastitis, which is a predominant form of protothecal disease in animals. Historically, identification of Prototheca spp. has relied upon phenotypic criteria; these were later replaced by molecular typing schemes, including DNA sequencing. However, the molecular markers interrogated so far, mostly located in the ribosomal DNA (rDNA) cluster, do not provide sufficient discriminatory power to distinguish among all Prototheca spp. currently recognized. Our study is the first attempt to develop a fast, reliable, and specific molecular method allowing identification of all Prototheca spp. We propose the mitochondrial cytb gene as a new and robust marker for diagnostics and phylogenetic studies of the Prototheca algae. The cytb gene displayed important advantages over the rDNA markers. Not only did the cytb gene have the highest discriminatory capacity for resolving all Prototheca species, but it also performed best in terms of technical feasibility, understood as ease of amplification, sequencing, and multiple alignment analysis. Based on the species-specific polymorphisms in the partial cytb gene, we developed a fast and straightforward PCR-restriction fragment length polymorphism (RFLP) assay for identification and differentiation of all Prototheca species described so far. The newly proposed method is advocated to be a new gold standard in diagnostics of protothecal infections in human and animal populations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Achlorophyllous unicellular microalgae of the genus Prototheca (Trebouxiophyceae, Chlorophyta) are the only known plants that cause infections in both humans and animals, collectively referred to as protothecosis. Human protothecosis, most commonly manifested as cutaneous, articular, and disseminated disease, is primarily caused by Prototheca wickerhamii, followed by Prototheca zopfii and, sporadically, by Prototheca cutis and Prototheca miyajii. In veterinary medicine, however, P. zopfii is a major pathogen responsible for bovine mastitis, which is a predominant form of protothecal disease in animals. Historically, identification of Prototheca spp. has relied upon phenotypic criteria; these were later replaced by molecular typing schemes, including DNA sequencing. However, the molecular markers interrogated so far, mostly located in the ribosomal DNA (rDNA) cluster, do not provide sufficient discriminatory power to distinguish among all Prototheca spp. currently recognized. Our study is the first attempt to develop a fast, reliable, and specific molecular method allowing identification of all Prototheca spp. We propose the mitochondrial cytb gene as a new and robust marker for diagnostics and phylogenetic studies of the Prototheca algae. The cytb gene displayed important advantages over the rDNA markers. Not only did the cytb gene have the highest discriminatory capacity for resolving all Prototheca species, but it also performed best in terms of technical feasibility, understood as ease of amplification, sequencing, and multiple alignment analysis. Based on the species-specific polymorphisms in the partial cytb gene, we developed a fast and straightforward PCR-restriction fragment length polymorphism (RFLP) assay for identification and differentiation of all Prototheca species described so far. The newly proposed method is advocated to be a new gold standard in diagnostics of protothecal infections in human and animal populations. |
Scientific interests