Biology subjects

Kanai, A.

Publications and source records attributed to Kanai, A..

25 records · Page 2Linked to original sources

bioRxiv2023

Diversification of Polynucleotide Kinase Clp1 Family Proteins and Their Possible Origins in Eukaryotic Evolution

The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5' end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species and identified a group of protist proteins that we consider to be the evolutionary origin of Clp1 family proteins. First, we detected an average of 4.2 Clp1 family genes in members of in the protist phylum Euglenozoa, arising from gene duplication. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. In a phylogenetic analysis of the PNK domain, Tb-Clp1-t2 mapped to the earliest position on the tree. Interestingly, Tb-Clp1-t1, for which no PNK activity was detected, was located on the phylogenetic tree near fungal Saccharomyces cerevisiae Clp1, which also lacks PNK activity. The analysis also revealed that in the higher eukaryotes, such as humans and plants, the Clp1 proteins diversified with the creation of isoforms by alternative splicing.

evolutionary biology↗

bioRxiv2022

Robust capability of renal tubule fatty acid uptake from apical and basolateral membranes in physiology and disease

Excess lipid accumulation is associated with obesity-related chronic kidney disease, but the mechanisms of fatty acid (FA) uptake have been poorly understood. To this end, we investigated how FAs are taken up by tubular epithelial cells (TECs) in mice by using in vivo FA tracing and histological methods. Immunohistochemistry showed that CD36, which is a well-known FA transporter, was abundantly expressed on the basolateral side of proximal TECs (PTECs). The uptake of 125I-BMIPP (a radiolabeled FA tracer) was significantly reduced in CD36-knockout kidneys at 1 min after injection. In vivo imaging with multiphoton microscopy revealed that BODIPY-C12 (a fluorescence-labeled FA tracer) accumulated on both the basolateral and apical sides of PTECs. Numerous lipid droplets accumulated in PTECs after accelerated lipolysis. Furthermore, PTEC-specific injury via diphtheria toxin (DT) injection in transgenic mice expressing the DT receptor resulted in a compensatory increase in lipid accumulation in downstream TECs. Importantly, urinary FAs were undetectable, even in mice and humans with remarkable albuminuria. Our data demonstrate that renal TECs take up FAs from blood (CD36-dependent) and primary urine (CD36-independent) and can store excess FAs as neutral lipids. The results further show that renal tubules have hitherto largely unappreciated mechanisms by which the excretion of FAs into the urine is avoided.

biochemistry↗

bioRxiv2022

Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

The Candidate Phyla Radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and often lack ribosomal proteins L1, L9, and/or L30, which are basically ubiquitous in ordinary (non-CPR) bacteria. Here, we comprehensively analyzed the genomic information of CPR bacteria and identified their unique properties. In the distribution of protein lengths in CPR bacteria, the peak was at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that CPR bacteria have smaller proteins on average, like symbiotic non-CPR bacteria. We found that ribosomal proteins L28, L29, L32, and L33 are also deleted in CPR bacteria, in a lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins in CPR differ, in part, from those of non-CPR bacteria, with missing regions or specific added region. We also found that several regions of the 16S, 23S, and 5S rRNAs are lacking in CPR bacteria and that the total predicted length of the three rRNAs in CPR bacteria is smaller than that in non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than in free-living non-CPR bacteria, with simplified surface structures.

bioinformatics↗

bioRxiv2021

Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes

Group II introns (G2Is) are self-splicing ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are considered an important factor in the evolution of prokaryotes, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative species had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative species had an average of 3.0 G2Is. The greatest number of G2Is per species was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1-U3) to the previous classification. This analysis suggested that about 30% of all IEPs are noncanonical IEPs. The number of G2Is per species was defined almost at the phylum level, and the type of IEP was associated as a factor in the G2I increase, i.e. there was an explosive increase in G2Is with bacterial C-type IEPs in the phylum Firmicutes and in G2Is with CL-type IEPs in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.

evolutionary biology↗

bioRxiv2021

HBO1-MLL interaction promotes AF4/ENL/P-TEFb-mediated leukemogenesis

Leukemic oncoproteins cause uncontrolled self-renewal of hematopoietic progenitors by aberrant gene activation, eventually causing leukemia. However, the molecular mechanism of aberrant gene activation remains elusive. Here, we showed that leukemic MLL fusion proteins associate with the HBO1 histone acetyltransferase (HAT) complex through their TRX2 domain. Among many MLL fusions, MLL-ELL particularly depended on its association with the HBO1 complex for leukemic transformation. The C-terminal portion of ELL provided a binding platform for multiple factors including AF4, EAF1 and p53. MLL-ELL activated gene expression by loading an AF4 /ENL/P-TEFb complex (AEP) onto the target promoters. The HBO1 complex promoted the use of AEP over EAF1 and p53. Moreover, the NUP98-HBO1 fusion protein exerted its oncogenic properties via interaction with MLL but not its intrinsic HAT activity. Thus, the interaction between HBO1 and MLL is an important nexus in leukemic transformation, which may serve as a therapeutic target for drug development.

cancer biology↗

bioRxiv2020

HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic pathways

HOXA9 is often highly expressed in leukemias. However, its precise roles in leukemogenesis remain elusive. Here, we show that HOXA9 maintains gene expression for multiple anti-apoptotic pathways to promote leukemogenesis. In MLL-rearranged leukemia, MLL fusion directly activates the expression of MYC and HOXA9. Combined expression of MYC and HOXA9 induced leukemia, whereas single gene transduction of either did not, indicating a synergy between MYC and HOXA9. HOXA9 sustained expression of the genes implicated to the hematopoietic precursor identity when expressed in hematopoietic precursors, but did not reactivate it once silenced. Among the HOXA9 target genes, BCL2 and SOX4 synergistically induced leukemia with MYC. Not only BCL2, but also SOX4 suppressed apoptosis, indicating that multiple anti-apoptotic pathways underlie cooperative leukemogenesis by HOXA9 and MYC. These results demonstrate that HOXA9 is a key transcriptional maintenance factor which promotes MYC-mediated leukemogenesis, potentially explaining why HOXA9 is highly expressed in many leukemias.

cancer biology↗

bioRxiv2018

Identification of PTBP1 responsible for caspase dependent YRNA cleavage

Some RNAs such as 28S rRNA, U1 snRNA, and Y RNAs are known to be cleaved during apoptosis. As the underlying mechanism is yet unclear, the functions and biological significance of RNA degradation in apoptosis remain elusive. We previously identified novel, functional small RNAs named AGO-taxis small RNA (ASR) that are specifically bound to AGO1. Here, we investigated ASR biogenesis, which appears to be non-canonical. Y RNAs, non-coding RNAs degraded during apoptosis, were identified as the precursors of several ASRs. Cell-free analysis combined with fractionation methods revealed that the apoptosis-specific biogenesis of ASRs or Y RNA degradation was induced by PTBP1--an endoribonuclease inhibitor of Y RNAs. PTBP1, a splicing factor, was truncated by caspase 3, which subsequently activated endoribonuclease to induce biogenesis of ASRs and Y RNA cleavage.

molecular biology↗