Biology subjects

Miwa, T.

Publications and source records attributed to Miwa, T..

4 recordsLinked to original sources

bioRxiv2024

Environmental DNA Surveys of Invertebrate Community on Forest Canopies Using Rainwater Analysis

Forest canopies, known for their high biodiversity, are essential for understanding forest ecosystems. Traditional methods for canopy surveys, such as tree climbing and canopy walkways, face challenges related to safety, cost, and time constraints. Environmental DNA (eDNA) analysis, which involves examining DNA from environmental samples, offers a promising alternative for these surveys. This study investigates the feasibility of using rainwater to collect eDNA from forest canopies, utilizing rains natural ability to wash away DNA from hard-to-reach areas. By comparing DNA analysis results from rainwater with conventional records obtained through visual and capture surveys, this research aims to validate the effectiveness and reliability of this method. Preliminary findings suggest that eDNA analysis from rainwater could provide an efficient approach to canopy biodiversity surveys, though further validation is required. This study marks an important first step towards developing eDNA analysis as a complementary tool for forest canopy research.

ecology↗

bioRxiv2023

Self-regulatory function of bacterial small heat shock protein IbpA through mRNA binding is conferred by a conserved arginine

Bacterial small heat shock proteins, IbpA and IbpB, co-aggregate with denatured proteins and recruit other chaperones for the processing of aggregates, thereby assisting in their refolding. In addition, as a recently revealed uncommon feature, Escherichia coli IbpA self-represses its own translation through interaction with the 5 untranslated region (UTR) of the ibpA mRNA, enabling IbpA to act as a mediator of negative feedback regulation. Although IbpA also suppresses the expression of IbpB, IbpB does not have the self-repression activity despite the two Ibps being highly homologous. This study demonstrates that the self-repression function of IbpA is conserved in other bacterial IbpAs. Moreover, a cationic residue-rich region in the -crystallin domain (ACD) of IbpA, which is not conserved in IbpB, is critical for the self-suppression activity. Notably, arginine 93 (R93) located within the ACD is an essential residue that cannot be replaced by the other 19 amino acids, including lysine. IbpA-R93 mutants completely lost the interaction with the 5 UTR of the ibpA mRNA but retained almost all of the chaperone activity to sequester denatured proteins. Taken together, the conserved Arg93-mediated translational control of IbpA through RNA binding would be beneficial for a rapid and massive supply of the chaperone on demand.

biochemistry↗

bioRxiv2023

The Escherichia coli small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ32

Small heat shock proteins (sHsps) act as ATP-independent chaperones that prevent irreversible aggregate formation by sequestering denatured proteins. IbpA, an Escherichia coli sHsp, functions not only as a chaperone but also as a suppressor of its own expression through posttranscriptional regulation, contributing to negative feedback regulation. IbpA also regulates the expression of its paralog, IbpB, in a similar manner, but the extent to which IbpA regulates other protein expressions is unclear. We have discovered that IbpA downregulates the expression of many Hsps by repressing the translation of the heat shock transcription factor {sigma}32. The IbpA regulation not only controls the {sigma}32 level but also contributes to the shut-off of the heat shock response. These results revealed an unexplored role of IbpA to regulate heat shock response at a translational level, which adds a new layer for tightly controlled and rapid expression of {sigma}32 on demand. Significance StatementTo survive during heat shock, cells have a mechanism to induce the synthesis of Hsps and to restore normal levels when the stress subsides. The molecular mechanisms of the heat shock response in E. coli have been extensively studied over the years. The master heat shock transcriptional regulator, {sigma}32, which is normally at low levels due to chaperone-mediated degradation, is increased upon heat shock. Our study has identified a previously unknown factor, IbpA, that regulates the level of {sigma}32 by suppressing its expression at a translational level, thereby contributing to the heat shock response regulation.

molecular biology↗

bioRxiv2020

Escherichia coli small heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at a translational level

Aggregation is an inherent characteristic of proteins. Risk management strategies to reduce aggregation are critical for cells to survive upon stresses that induce aggregation. Cells cope with protein aggregation by utilizing a variety of chaperones, as exemplified by heat-shock proteins (Hsps). The heat stress-induced expression of IbpA and IbpB, small Hsps in Escherichia coli, is regulated by the {sigma}32 heat-shock transcriptional regulator and the temperature-dependent translational regulation via mRNA heat fluctuation. We found that, even without heat stress, either the expression of aggregation-prone proteins or the ibpA gene deletion profoundly increases the expression of IbpA. Combined with other evidence, we propose novel mechanisms for the regulation of the small Hsp expression. Oligomeric IbpA self-represses the ibpA/ibpB expression at the translational level, but the self-repression is relieved by the sequestration of IbpA into protein aggregates. Thus, the function of IbpA as a chaperone to form co-aggregates is harnessed as an aggregation sensor to tightly regulate the IbpA level. Since the excessive preemptive supply of IbpA in advance of stress is harmful, the prodigious and rapid expression of IbpA/IbpB on demand is necessary for IbpA to function as a first line of defense against acute protein aggregation. Author summaryAll organisms have protein quality control systems against stresses disturbing cellular protein homeostasis (proteostasis). The systems have multiple stages: folding, degradation, and sequestration. Sequestration of denatured proteins is the first step to support other maintenance strategies. Small heat shock proteins (sHsps), which are well-conserved chaperones, are representative "sequestrases" that co-aggregate with denatured proteins. We found that IbpA, an Escherichia coli sHsp, is a direct mediator for negative feedback regulation at the translational level. Recruitment of IbpA into the protein aggregates relieves the ibpA expression suppression. This novel mechanism of IbpA as an aggregation-sensor tightly regulates the IbpA level, enabling the sHsp to function as a sequestrase upon aggregation stress.

biochemistry↗