Biology subjects

Nikolov, L. A.

Publications and source records attributed to Nikolov, L. A..

3 recordsLinked to original sources

bioRxiv2024

Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

O_LIPremise - Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it is difficult to assess which tool to best use for plant species, which commonly have complex genomic histories. C_LIO_LIMethods - We explored the performance of four orthology inference algorithms - OrthoFinder, SonicParanoid, Broccoli, and OrthNet - on eight Brassicaceae genomes in two groups: one group comprising only diploids and another set comprising the diploids, two mesopolyploids, and one recent hexaploid genome. C_LIO_LIResults - Orthogroup compositions reflect the species ploidy and genomic histories. Additionally, the diploid set had a higher proportion of identical orthogroups. While the diploid+higher ploidy set had a lower proportion of orthogroups with identical compositions, the average degree of similarity between the orthogroups was not different from the diploid set. C_LIO_LIDiscussion - Three algorithms - OrthoFinder, SonicParanoid, and Broccoli - are helpful for initial orthology predictions. Results from OrthNet were generally an outlier but could provide detailed information about gene colinearity. With our Brassicaceae dataset, slight discrepancies were found across the orthology inference algorithms, necessitating additional analyses, such as tree inference to fine-tune results. C_LI

genomics↗

bioRxiv2023

Toxoplasma gondii encodes an array of TBC-domain containing proteins including an essential regulator that targets Rab2 in the secretory pathway

Toxoplasma gondii resides in its intracellular niche by employing a series of specialized secretory organelles that play roles in invasion, host-cell manipulation and parasite replication. Rab GTPases are major regulators of the parasites secretory traffic that function as nucleotide dependent molecular switches to control vesicle trafficking. While many of the Rab proteins have been characterized in T. gondii, precisely how these Rabs are regulated remains poorly understood. To better understand the parasites secretory traffic, we investigated the entire family of Tre2-Bub2-Cdc16 (TBC)-domain containing proteins, which are known to be involved in vesicle fusion and secretory protein trafficking. We first determined the localization of all 18 TBC-domain containing proteins to discrete regions of the secretory pathway or other vesicles in the parasite. We then use an auxin-inducible degron approach to demonstrate that the protozoan-specific TgTBC9 protein that localizes to the ER is essential for parasite survival. Knockdown of TgTBC9 results in parasite growth arrest and affects the organization of the ER and Golgi apparatus. We show that the conserved dual-finger active site in the TBC-domain of the protein is critical for its GTPase-activating protein (GAP) function and that the P. falciparum orthologue of TgTBC9 can rescue the lethal knockdown. We additionally show by immunoprecipitation and yeast two hybrid analyses that TgTBC9 directly binds Rab2, indicating that this TBC-Rab pair controls ER to Golgi traffic in the parasite. Together, these studies identify the first essential TBC protein described in any protozoan, provide new insight into intracellular vesicle trafficking in T. gondii, and reveal promising targets for the design of novel therapeutics that can specifically target apicomplexan parasites.

microbiology↗

bioRxiv2021

INDEHISCENT regulates explosive seed dispersal

How traits evolve to produce novelty or stasis is an open question in biology. We investigate this question in Cardamine hirsuta, a relative of Arabidopsis thaliana that employs explosive fracture to disperse its seeds. This trait evolved through key morphomechanical innovations that distinguish the otherwise very similar, dehiscent fruit of these two species. Using CRISPR/Cas9, we show that dehiscence zone formation is absolutely required for explosive fracture in C. hirsuta, and is controlled by the bHLH transcription factor INDEHISCENT (IND). Using mutant screens, we identified the MADS-box transcription factor FRUITFULL (FUL) as a negative regulator of IND in C. hirsuta. Although FUL function is conserved in C. hirsuta, the consequences of IND mis-expression differ in ful mutants of C. hirsuta versus A. thaliana. In ful mutants of both species, valve tissue is replaced by dehiscence zone tissue, which comprises two distinct cell types: lignified layer and separation layer cells. While A. thaliana ful mutants develop stunted fruit with ectopic lignified layer cells, C. hirsuta ful mutants have elongated fruit with ectopic separation layer cells. We show that IND dose determines the proportion of these two cell types in ectopic dehiscence zones. We also show that the extent of ectopic lignification caused by IND mis-expression determines fruit length. Our findings indicate developmental system drift in the conserved gene network patterning dehiscent fruit in two related Brassicaceae species.

plant biology↗