Biology subjects

Tian, X.

Publications and source records attributed to Tian, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

Lithocholic acid targets TULP3 to activate sirtuins and AMPK to retard ageing

Lithocholic acid (LCA), accumulated in the body during calorie restriction (CR), can confer administered metazoans with the ability to activate AMP-activated protein kinase (AMPK) and retard ageing. However, how LCA is signalled to activate AMPK and elicit the biological effects is unclear. Here, we show that LCA can enhance sirtuins (SIRTs) to deacetylate and subsequently inhibit vacuolar H+-ATPase (v-ATPase), thereby triggering AMPK activation via the lysosomal glucose-sensing pathway. Through proteomic analysis of SIRT1-coimmunoprecipitated proteins, we identify and validate that TUB like protein 3 (TULP3) is a constitutive component of SIRTs. Surprisingly, we found that TULP3 is an LCA receptor, and that the LCA-bound TULP3 activates SIRTs. The activated SIRTs in turn deacetylate the V1E1 subunit of v-ATPase on K52, K99 and K191 residues. Muscle-specific expression of the 3KR mutant of V1E1, mimicking the deacetylated state, dominantly activates AMPK and rejuvenates muscles in aged mice. Moreover, LCA once administered also activates AMPK and extends lifespan and healthspan in nematodes and flies, depending on the TULP3 homologues tub-1 and ktub, respectively. Our study thus elucidates that LCA triggers the TULP3-sirtuin-v-ATPase- AMPK route to manifest benefits of calorie restriction.

physiology↗

bioRxiv2023

Lithocholic acid phenocopies rejuvenating and life-extending effects of calorie restriction

Calorie restriction (CR) is a dietary intervention to promote health and longevity. CR causes various metabolic changes in both the production and circulation of metabolites; however, it remains unclear which of the changed metabolite(s) can account for the physiological benefits of CR. Through metabolomic analysis of metabolites undergoing abundance changes during CR and subsequent functional validation, we found that lithocholic acid (LCA) is the only metabolite that alone can recapitulate the effects of CR, including activation of AMPK and the rejuvenating effects of muscle regeneration, grip strength and running capacity in mice. Interestingly, LCA also activates AMPK and exerts life- and health-extending effects in Caenorhabditis elegans and Drosophila melanogaster, indicating that these animal models are able to transmit the signalling of LCA once administered. Knockout of AMPK abrogates LCA-induced phenotypes, in nematodes and flies, as well as in mice. Together, we have identified that administration of the CR-upregulated metabolite LCA alone can confer anti-ageing benefits to metazoans, in an AMPK-dependent manner.

physiology↗

bioRxiv2023

Manual gestures help learn lexical stress of foreign languages by precise modulation of early auditory neural responses

Gestures accompany speech and facilitate communication and learning. Most previous studies have demonstrated the effects of gestures on learning semantics, yet how gestures facilitate learning low- and intermediate-level speech features is unclear. The present study investigated the effects of manual gestures on learning lexical stress, a phonological-lexical feature that is foreign to native Mandarin speakers. Across a series of experiments, we demonstrated that the gestures with representational relations to auditory stimuli in terms of covaried amplitude modulation facilitated the learning of lexical stress for both familiar (English) and unknown (Russian) languages, but not for pseudowords that lack phonotactic properties. Interestingly, gestures with amplitude trajectory matching the stress benefited the learning of trained words, whereas gestures that only matched the timing of syllable segments but not amplitude variation generalized the learning effects to untrained stimuli. Furthermore, in the EEG experiment, we found that gesture-accompanied learning was associated with power increase and inter-trial phase coherence (ITC) decrease in the theta band at the time windows corresponding to the stress positions. These results suggest that the facilitatory effects of gestures on lexical stress learning depend on the specificity of cross-modal feature mapping at the phonological level, mediated by the neural modulation in early perceptual responses.

neuroscience↗

bioRxiv2023

Local two-photon excitation reveals the mechanism of mitochondrial Ca2+ release

Mitochondrial Ca2+ (mitoCa2+) simultaneously implicates respiration, mitochondrial physiology, and cell signaling, which prevents the disentanglement of mitoCa2+ from those complex processes. Although mitochondria have long been recognized as temporary Ca2+ buffer, how mitoCa2+ is regulated and released remains unclear. In this study, we report a specific photochemical excitation to flavoproteins in single-mitochondrion tubulars by a tightly-focused femtosecond laser that triggers local mitoCa2+ transients, without any extra-mitochondrial Ca2+ involved. The two-photon excitation to complex I and II accelerates the entire electron transport chain (ETC) and promotes ATP synthesis. Free mitoCa2+ is thus released from the Ca2+-phosphate ion (Pi) complexes at complex V in mitochondrial matrix during ATP synthesis to form mitoCa2+ transients there. The abnormal mitoCa2+ signaling by knockdown of ATP synthase subunit affects cell proliferation, apoptosis, and mitophagy. Our results reveal mitoCa2+ is released and regulated by ETC and ATP synthesis rather than the reverse. Mitochondria are multi-functional units to simultaneously produce energy and coordinate molecular signaling for cells. The key process of metabolism, tricarboxylic acid (TCA) cycle, is continuously ongoing in mitochondrial matrix and generates reducing equivalents for subsequent electron transfer (Martinez-Reyes and Chandel, 2020; Martinez-Reyes et al., 2016). The respiration is accomplished by electron transport chain (ETC) in the inner mitochondrial membrane (IMM) (Marreiros et al., 2016). Mitochondria regulate a series of signaling cascades to mediate apoptosis, autophagy, and cell senescence (Galluzzi et al., 2014; Rasola and Bernardi, 2011; Ziegler et al., 2021). Biosynthesis of some amino acids and nucleotides also takes place in mitochondria (Ahn and Metallo, 2015; Li and Hoppe, 2023). Those processes are involved with each other through complex crosstalk and feedbacks. Mitochondria have long been recognized as Ca2+ buffer to temporarily deposit abnormal cytosolic Ca2+ for cellular Ca2+ homeostasis (Garbincius and Elrod, 2022; Kirichok et al., 2004; Lambert et al., 2019). However, the Ca2+ entry into mitochondria definitely influence those mitochondrial processes and functions (Garbincius and Elrod, 2022). The acute and direct consequences of Ca2+ entry into mitochondria are found as depolarization of mitochondrial membrane potential (MMP). If the cellular Ca2+ level is too high, mitochondria may become damaged and dysfunctional. Mitophagy/autophagy and even apoptosis are initiated (Galluzzi et al., 2014; Lou et al., 2020; Rasola and Bernardi, 2011). Moreover, Ca2+ in mitochondrial matrix (mitoCa2+) takes an essential role in quite a few physiological processes including mitochondrial fission and fusion, cell development, and proliferation (Doonan et al., 2014; Singh and Mabalirajan, 2021; Steffen and Koehler, 2018). The respiration is also believed to be related to mitoCa2+ (Glancy and Balaban, 2012; Wescott et al., 2019). Technically, perturbation to mitoCa2+ affects most mitochondrial processes and physiology, which makes it quite difficult to interrogate how Ca2+ is regulated and released in mitochondria. So far, the regulation of mitoCa2+ remains in mist. In this study, we report a single-mitochondrion photochemical process by tightly-focused femtosecond laser that specifically excites complex I and II by two-photon excitation and accelerate ETC. Free mitoCa2+ is released from Ca2+-phosphate ion (Pi) complexes by ATP synthesis at complex V in mitochondria. These results clarify the mechanism of mitoCa2+ regulation and provide further insights in the relationship between mitoCa2+ and respiration.

cell biology↗

bioRxiv2023

Regulation of Lung Immune Tone by the Gut-Lung Axis via Dietary Fiber, Gut Microbiota, and Short-Chain Fatty Acids

Lung immune tone, i.e. the immune state of the lung, can vary between individuals and over a single individuals lifetime, and its basis and regulation in the context of inflammatory responses to injury is poorly understood. The gut microbiome, through the gut-lung axis, can influence lung injury outcomes but how the diet and microbiota affect lung immune tone is also unclear. We hypothesized that lung immune tone would be influenced by the presence of fiber-fermenting short-chain fatty acid (SCFA)-producing gut bacteria. To test this hypothesis, we conducted a fiber diet intervention study followed by lung injury in mice and profiled gut microbiota using 16S sequencing, metabolomics, and lung immune tone. We also studied germ-free mice to evaluate lung immune tone in the absence of microbiota and performed in vitro mechanistic studies on immune tone and metabolic programming of alveolar macrophages exposed to the SCFA propionate (C3). Mice on high-fiber diet were protected from sterile lung injury compared to mice on a fiber-free diet. This protection strongly correlated with lower lung immune tone, elevated propionate levels and enrichment of specific fecal microbiota taxa; conversely, lower levels of SCFAs and an increase in other fatty acid metabolites and bacterial taxa correlated with increased lung immune tone and increased lung injury in the fiber-free group. In vitro, C3 reduced lung alveolar macrophage immune tone (through suppression of IL-1{beta} and IL-18) and metabolically reprogrammed them (switching from glycolysis to oxidative phosphorylation after LPS challenge). Overall, our findings reveal that the gut-lung axis, through dietary fiber intake and enrichment of SCFA-producing gut bacteria, can regulate innate lung immune tone via IL-1{beta} and IL-18 pathways. These results provide a rationale for the therapeutic development of dietary interventions to preserve or enhance specific aspects of host lung immunity.

immunology↗

bioRxiv2023

O-GlcNAcylation of Keratin 18 coordinates TCA cycle to promote cholangiocarcinoma progression

Glycosylation in human cholangiocarcinoma (CCA) actively contributes to pathophysiological steps of tumor progression. Of note is the dynamic modification of proteins by O-linked {beta}-N-acetyl-glucosamine (O-GlcNAcylation) that modulates various tumor-associated biological activities. By using a cutting-edge chemical proteomic methodology for intact glycopeptide analysis, we show herein that O-GlcNAcylation of Keratin 18 (K18) coordinates the tricarboxylic acid (TCA) cycle enzymes, namely isocitrate dehydrogenases (IDHs), to promote CCA progression. Mechanistically, site-specific O-GlcNAcylation of K18 on Ser 30 stabilizes K18, which benefits the expression of cell cycle checkpoints to enhance cell cycle progression and cell growth. Interaction with IDHs down-regulates the level of citrate and isocitrate, while up-regulates the level of -ketoglutarate (-KG). Our study thus expands the current understanding of protein O-GlcNAcylation, and adds another dimension of complexity to post-translational control over metabolism and tumorigenesis.

cancer biology↗

bioRxiv2023

AMPK targets PDZD8 to trigger carbon source shift to glutamine

The shift of carbon utilisation from glucose to other nutrients is a fundamental metabolic adaptation to cope with the decreased glucose oxidation during fasting or starvation1. AMP-activated protein kinase (AMPK) plays crucial roles in manifesting physiological benefits accompanying glucose starvation or calorie restriction2. However, the underlying mechanisms are unclear. Here, we show that low glucose-induced activation of AMPK plays a decisive role in the shift of carbon utilisation from glucose to glutamine. We demonstrate that endoplasmic reticulum (ER)-localised PDZD8, which we identify to be a new substrate of AMPK, is required for the glucose starvation-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527), and promotes it to interact with and activate the mitochondrial glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis3-5, and as a result the ER-mitochondria contact is strengthened. In vivo, PDZD8 enhances glutaminolysis, and triggers mitohormesis that is required for extension of lifespan and healthspan in Caenorhabditis elegans subjected to glucose starvation or caloric restriction. Muscle-specific re-introduction of wildtype PDZD8, but not the AMPK-unphosphorylable PDZD8-T527A mutant, to PDZD8-/- mice is able to rescue the increase of glutaminolysis, and the rejuvenating effects of caloric restriction in aged mice, including grip strength and running capacity. Together, these findings reveal an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis and executes the anti-ageing effects of calorie restriction by promoting inter-organelle crosstalk between ER and mitochondria.

cell biology↗

bioRxiv2023

SALL4B, not targeted by IMiD, is important for SALL4-mediated tumorigenesis

Immunomodulatory (IMiD) drugs have shown a prominent therapeutic activity in hematologic malignancies; however, their usage in solid tumors is limited. The oncofetal protein SALL4 is essential for cancer cell survival. While IMiDs can induce SALL4 degradation, they fail to induce cell death in SALL4-expressing cancer cell lines. Here, we observed that this inefficacy arose from their selective degradation of the long SALL4 isoform, while sparing the short SALL4B isoform. Selective silencing of SALL4B phenocopied total SALL4 depletion by inducing cancer apoptosis, underscoring the critical role of SALL4B in cancer maintenance. Recognizing that IMiDs cant degrade SALL4B, we performed a high-throughput screen to identify compound(s) that could achieve this. We identified a small molecule compound that degrades both SALL4 isoforms with enhanced potency towards SALL4B in a cereblon- and proteasome-dependent manner. This compound suppressed cancer cell proliferation and attenuated tumor development in both cell line and patient-derived xenograft models. Transcriptomic analyses further revealed convergent effects of genetic and pharmacologic SALL4B depletion on DNA damage response and replication pathways. Together, these findings identify SALL4B as the therapeutically relevant isoform in SALL4-dependent cancers and establish isoform-aware targeted degradation as a strategy to overcome the limitation of IMiDs in solid tumors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/548071v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@99670dorg.highwire.dtl.DTLVardef@13ca58forg.highwire.dtl.DTLVardef@998e7eorg.highwire.dtl.DTLVardef@15a1875_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract | Identification of QE: a non-IMiDs degrader capable of degrading both SALL4A and SALL4B, triggers anti-cancer effects beyond IMiDs, and Impacts of QE on Key Validated SALL4B Targets and Pathways C_FIG

cancer biology↗

bioRxiv2023

Direct interhemispheric cortical communication via thalamic commissures: a new white-matter pathway in the primate brain

Cortical neurons of eutherian mammals project to the contralateral hemisphere, crossing the midline primarily via the corpus callosum and the anterior, posterior, and hippocampal commissures. We recently reported an additional commissural pathway in rodents, termed the thalamic commissures (TCs), as another interhemispheric axonal fiber pathway that connects cortex to the contralateral thalamus. Here, we demonstrate that TCs also exist in primates and characterize the connectivity of these pathways with high-resolution diffusion-weighted magnetic resonance imaging, viral axonal tracing, and functional MRI. We present evidence of TCs in both New World (Callithrix jacchus and Cebus apella) and Old World primates (Macaca mulatta). Further, like rodents, we show that the TCs in primates develop during the embryonic period, forming anatomical and functionally active connections of the cortex with the contralateral thalamus. We also searched for TCs in the human brain, showing their presence in humans with brain malformations, although we could not identify TCs in healthy subjects. These results pose the TCs as an important fiber pathway in the primate brain, allowing for more robust interhemispheric connectivity and synchrony and serving as an alternative commissural route in developmental brain malformations. Significance statementBrain connectivity is a central topic in neuroscience. Understanding how brain areas can communicate allows for the comprehension of brain structure and function. We have described in rodents a new commissure pathway that connects the cortex to the contralateral thalamus. Here, we investigate whether this pathway exists in non-human primates and humans. The presence of these commissures poses the TCs as an important fiber pathway in the primate brain, allowing for more robust interhemispheric connectivity and synchrony and serving as an alternative commissural route in developmental brain malformations.

neuroscience↗

bioRxiv2023

Impaired motor-to-sensory transformation mediates auditory hallucinations

Distinguishing reality from hallucinations requires efficient monitoring of agency. It has been hypothesized that a copy of motor signals, termed efference copy (EC) or corollary discharge (CD), suppresses sensory responses to yield a sense of agency; impairment of the inhibitory function leads to hallucinations. However, how can the sole absence of inhibition yield positive symptoms of hallucinations? We hypothesize that selective impairments in functionally distinct signals of CD and EC during motor-to-sensory transformation cause the positive symptoms of hallucinations. In an electroencephalography (EEG) experiment with a delayed articulation paradigm in schizophrenic patients with (AVHs) and without auditory verbal hallucinations (non-AVHs), we found that preparing to speak without knowing the contents (general preparation) did not suppress auditory responses in both patient groups, suggesting the absent of inhibitory function of CD. Whereas, preparing to speak a syllable (specific preparation) enhanced the auditory responses to the prepared syllable in non-AVHs, whereas AVHs showed enhancement in responses to unprepared syllables, opposite to the observations in the normal population, suggesting that the enhancement function of EC is not precise in AVHs. A computational model with a virtual lesion of an inhibitory inter-neuron and disproportional sensitization of auditory cortices fitted the empirical data and further quantified the distinct impairments in motor-to-sensory transformation in AVHs. These results suggest that broken CD plus noisy EC causes erroneous monitoring on the imprecise generation of internal auditory representation and yields auditory hallucinations. Specific impairments in functional granularity of motor-to-sensory transformation mediate positivity symptoms of agency abnormality in mental disorders.

neuroscience↗

bioRxiv2023

Effects of growth feedback on gene circuits: A dynamical understanding

The successful integration of engineered gene circuits into host cells remains a significant challenge in synthetic biology due to circuit-host interactions, such as growth feedback, where the circuit influences cell growth and vice versa. Understanding the dynamics of circuit failures and identifying topologies resilient to growth feedback are crucial for both fundamental and applied research. Utilizing transcriptional regulation circuits with adaptation as a paradigm, we systematically study more than four hundred topological structures and uncover various categories of failures. Three dynamical mechanisms of circuit failures are identified: continuous deformation of the response curve, strengthened or induced oscillations, and sudden switching to coexisting attractors. Our extensive computations also uncover a scaling law between a circuit robustness measure and the strength of growth feedback. Despite the negative effects of growth feedback on the majority of circuit topologies, we identify several circuits that maintain optimal performance as designed, a feature important for applications.

synthetic biology↗

bioRxiv2023

SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality

Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and background signal readout makes it challenging to achieve absolute glycan quantification. Here we develop SeMOE, a selenosugar-based metabolic oligosaccharide engineering strategy that combines elemental analysis and MOE to enable the absolute quantification and mass spectrometric imaging of glycome in a concise procedure. We demonstrate that SeMOE probes allow for perception, absolute quantification and visualization of glycans in diverse biological contexts. We demonstrate that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. We further show the anti-cancer potentiality of SeMOE probes. SeMOE thus provides a convenient and simplified method to "see more" of the glyco-world.

bioengineering↗

bioRxiv2023

DNA repair and anti-cancer mechanisms in the longest-living mammal: the bowhead whale

At over 200 years, the maximum lifespan of the bowhead whale exceeds that of all other mammals. The bowhead is also the second-largest animal on Earth, reaching over 80,000 kg1. Despite its very large number of cells and long lifespan, the bowhead is not highly cancer-prone, an incongruity termed Petos Paradox2. This phenomenon has been explained by the evolution of additional tumor suppressor genes in other larger animals, supported by research on elephants demonstrating expansion of the p53 gene3-5. Here we show that bowhead whale fibroblasts undergo oncogenic transformation after disruption of fewer tumor suppressors than required for human fibroblasts. However, analysis of DNA repair revealed that bowhead cells repair double strand breaks (DSBs) and mismatches with uniquely high efficiency and accuracy compared to other mammals. The protein CIRBP, implicated in protection from genotoxic stress, was present in very high abundance in the bowhead whale relative to other mammals. We show that CIRBP and its downstream protein RPA2, also present at high levels in bowhead cells, increase the efficiency and fidelity of DNA repair in human cells. These results indicate that rather than possessing additional tumor suppressor genes as barriers to oncogenesis, the bowhead whale relies on more accurate and efficient DNA repair to preserve genome integrity. This strategy which does not eliminate damaged cells but repairs them may be critical for the long and cancer-free lifespan of the bowhead whale.

cancer biology↗

bioRxiv2023

Electrophysiological hallmarks for event relations and event roles in working memory

The ability to maintain events (i.e. interactions between/among objects) in working memory is crucial for our everyday cognition, yet the format of this representation is poorly understood. The current ERP study was designed to answer two questions: How is maintaining events (e.g., the tiger hit the lion) neurally different from maintaining item coordinations (e.g., the tiger and the lion)? That is, how is the event relation (present in events but not coordinations) represented? And how is the agent, or initiator of the event encoded differently from the patient, or receiver of the event during maintenance? We used a novel picture-sentence match-across-delay approach in which the working memory representation was pinged during the delay, in two ERP experiments with Chinese and English materials. First, we found that maintenance of events elicited a long-lasting late sustained difference in posterior-occipital electrodes relative to non-events. This effect resembled the negative slow wave reported in previous studies of working memory, suggesting that the maintenance of events in working memory may impose a higher cost compared to coordinations. Second, in order to elicit a hallmark for agent vs. patient representation in working memory, we pinged agent or patient characters during the delay. Although planned comparisons did not reveal significant differences in the ERPs elicited by the agent pings vs. patient pings, we found that the ping appeared to dampen the ongoing sustained difference, suggesting a shift from sustained activity to activity silent mechanisms. These results represent one of the uses of ERPs to elucidates the format of neural representation for events in working memory.

neuroscience↗

bioRxiv2023

Increased hyaluronan by naked mole-rat HAS2 extends lifespan in mice

Abundant high molecular weight hyaluronic acid (HMW-HA) contributes to cancer resistance and possibly longevity of the longest-lived rodent, the naked mole-rat1, 2. To study whether the benefits of HMW-HA could be transferred to other animal species, we generated a transgenic mouse overexpressing naked mole-rat hyaluronic acid synthase 2 gene (nmrHAS2). nmrHAS2 mice showed increase in hyaluronan levels in several tissues, and lower incidence of spontaneous and induced cancer, extended lifespan and improved healthspan. The transcriptome signature of nmrHAS2 mice shifted towards that of longer-lived species. The most striking change observed in nmrHAS2 mice was attenuated inflammation across multiple tissues. HMW-HA reduced inflammation via several pathways including direct immunoregulatory effect on immune cells, protection from oxidative stress, and improved gut barrier function during aging. These findings demonstrate that the longevity mechanism that evolved in the naked mole-rat can be exported to other species, and open new avenues for using HMW-HA to improve lifespan and healthspan.

physiology↗

bioRxiv2023

Human Attention during Goal-directed Reading Comprehension Relies on Task Optimization

The computational principles underlying attention allocation in complex goal-directed tasks remain elusive. Goal-directed reading, i.e., reading a passage to answer a question in mind, is a common real-world task that strongly engages attention. Here, we investigate what computational models can explain attention distribution in this complex task. We show that the reading time on each word is predicted by the attention weights in transformer-based deep neural networks (DNNs) optimized to perform the same reading task. Eye-tracking further reveals that readers separately attend to basic text features and question-relevant information during first-pass reading and rereading, respectively. Similarly, text features and question relevance separately modulate attention weights in shallow and deep DNN layers. Furthermore, when readers scan a passage without a question in mind, their reading time is predicted by DNNs optimized for a word prediction task. Therefore, we offer a computational account of how task optimization modulates attention distribution during real-world reading.

neuroscience↗

bioRxiv2023

SEQUENCE VS. STRUCTURE: DELVING DEEP INTO DATA DRIVEN PROTEIN FUNCTION PREDICTION

AO_SCPLOWBSTRACTC_SCPLOWPredicting protein function is a longstanding challenge that has significant scientific implications. The success of amino acid sequence-based learning methods depends on the relationship between sequence, structure, and function. However, recent advances in AlphaFold have led to highly accurate protein structure data becoming more readily available, prompting a fundamental question: given sufficient experimental and predicted structures, should we use structure-based learning methods instead of sequence-based learning methods for predicting protein function, given the intuition that a proteins structure has a closer relationship to its function than its amino acid sequence? To answer this question, we explore several key factors that affect function prediction accuracy. Firstly, we learn protein representations using state-of-the-art graph neural networks (GNNs) and compare graph construction(GC) methods at the residue and atomic levels. Secondly, we investigate whether protein structures generated by AlphaFold are as effective as experimental structures for function prediction when protein graphs are used as input. Finally, we compare the accuracy of sequence-only, structure-only, and sequence-structure fusion-based learning methods for predicting protein function. Additionally, we make several observations, provide useful tips, and share code and datasets to encourage further research and enhance reproducibility.

bioinformatics↗

bioRxiv2023

Duckweed evolution: from land back to water

Terrestialization is supposedly an important evolutionary process plant experience. However, directions of land back to water acquired little attention. Here we integrate multiproxy evidence to elucidate the evolution of duckweed. Three genera of duckweed show chronologically gradient degeneration in roots structure and stomatal function and decrease in lignocellulose content, accompanied by gradual contraction in relevant gene numbers and/or decline in transcription. The gene numbers in the main phytohormonal pathway are also gradually decreased. The co-action of auxin and rhizoid development gene causes a gradual decrease in adventitious roots. The significant expansion of the flavonoid pathway is also related to the adaptation of duckweed to floating growth. This study reconstructs the evolution history of duckweeds from land back to water, reverse to that of early land plants. SummaryWith terrestrialization being the popularly acknowledged plant evolutionary process, little is known about the evolution of higher plant from land back to water. Here we integrate multiproxy evidence to elucidate the gradual reverse evolution of duckweed. Three genera of duckweed show chronologically gradient degeneration in the structure of roots, the function of stomata, and decrease in lignocellulose content, accompanied by gradient contraction in relevant gene numbers and/or decline in transcript expression. The gene numbers in the main phytohormonal pathway are also gradually decreased. The co-action of auxin and rhizoid development gene causes a gradual decrease in adventitious roots. The significant expansion of the flavonoid pathway is also highly related to the adaptation of duckweed to floating growth. Our study combined with the fossil evidence reconstruct the evolution history of duckweeds from land back to water, reverse to that of early land plants. This study reconstructed the process of how a land plant returns to water, a reverse evolutionary approach which is different from what we studied in textbook about plant terrestrialization. This finding could be helpful for us to deeply and widely understand the adaptation of plant to the environment, and to expand and deepen the knowledge of evolution theory.

evolutionary biology↗