Biology subjects

Gu, L.

Publications and source records attributed to Gu, L..

98 records · Page 6Linked to original sources

bioRxiv2019

The YdiU Domain Modulates Bacterial Stress Signaling through UMPylation

Sensing stressful conditions and adjusting cellular metabolism to adapt to the environment is essential for bacteria to survive in variable situations. Here, we describe a new stress-related protein YdiU, and characterize YdiU as an enzyme that catalyzes the covalent attachment of uridine 5-monophosphate to a protein tyrosine/histidine residue--a novel modification defined as UMPylation. Mn2+ serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn2+-binding converts YdiU to an aggregate-prone state facilitating the recruitment of chaperones. The UMPylation of chaperones prevents them from binding co-factors or clients, thereby impairing their function. Consistent with the recent finding that YdiU acts as an AMPylator, we further demonstrate that the self-AMPylation of YdiU padlocks its chaperone-UMPylation activity. The detailed mechanism is proposed based on Apo-YdiU, YdiU-ATP, YdiU-AMP crystal structures and molecular dynamics simulation models of YdiU-UTP and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation. HighlightsO_LIYdiU involves in stress-resistance of Salmonella. C_LIO_LIYdiU mediates protein UMPylation in a Mn2+-dependent manner. C_LIO_LIStructural insights into YdiU-mediated UMPylation. C_LIO_LIUMPylation of chaperones by YdiU modulates their function. C_LI

biochemistry↗

bioRxiv2019

Developmentally Regulated Genome Editing in Terminally Differentiated N2-Fixing Heterocysts of Anabaena cylindrica ATCC 29414

Some vegetative cells of Anabaena cylindrica are programed to differentiate semi-regularly spaced, single heterocysts along filaments. Since heterocysts are terminally differentiated non-dividing cells, with the sole known function for solar-powered N2-fixation, is it necessary for a heterocyst to retain the entire genome ({approx}7.1 Mbp) from its progenitor vegetative cell? By sequencing the heterocyst genome, we discovered and confirmed that at least six DNA elements ({approx}0.12 Mbp) are deleted during heterocyst development. The six-element deletions led to the restoration of five genes (nifH1, nifD, hupL, primase P4 and a hypothetical protein gene) that were interrupted in vegetative cells. The deleted elements contained 172 genes present in the genome of vegetative cells. By sequence alignments of intact nif genes (nifH, nifD and hupL) from N2-fixing cyanobacteria (multicellular and unicellular) as well as other N2-fixing bacteria (non-cyanobacteria), we found that interrupted nif genes all contain the conserved core sequences that may be required for phage DNA insertion. Here, we discuss the nif genes interruption which uniquely occurs in heterocyst-forming cyanobacteria. To our best knowledge, this is first time to sequence the genome of heterocyst, a specially differentiated oxic N2-fixing cell. This research demonstrated that (1) different genomes may occur in distinct cell types in a multicellular bacterium; and (2) genome editing is coupled to cellular differentiation and/or cellular function in a heterocyst-forming cyanobacterium.

microbiology↗

bioRxiv2019

Unicellular Cyanobacteria Exhibit Light-Driven, Oxygen-Tolerant, Constitutive Nitrogenase Activity Under Continuous Illumination

Cyanobacteria have played a profound role in shaping the biosphere, most notably through the Great Oxygenation Event (GOE) with the advent of photosynthesis1. Cyanobacteria also contribute to global primary production through biological nitrogen fixation (BNF) using nitrogenase2,3, an oxygen-labile enzyme complex that evolutionarily predates the GOE4. Current literature reports nitrogenase activity in unicellular cyanobacteria is protected from oxygen through diurnal separation of photosynthesis and BNF5. However, historic conditions of continuous-light and warm temperature at polar latitudes during the Triassic and Cretaceous may have created a selective advantage amongst unicellular cyanobacteria for non-temporal mechanisms of maintaining nitrogenase activity in the presence of oxygen. Here we report constitutive nitrogenase activity concurrent with a net-gain of oxygen through photosynthesis in a continuous-light adapted culture of the unicellular cyanobacteria, Cyanothece sp. ATCC 51142. Nitrogenase activity in the adapted culture exhibited dependence on light and an increased resilience to artificially raised oxygen-tension compared to traditional culture. We predict cyanobacteria closely related to Cyanothece sp. ATCC 51142 also possess this physiology and found an accessory predicted proteome with functional relevance. This work provides a model of light-driven, oxygen-tolerant, constitutive nitrogenase activity and suggests this physiology may be conserved in closely related unicellular diazotrophic cyanobacteria with implications for primary production in polar ecosystems and potential biotechnological application in sustainable agriculture production.

microbiology↗

bioRxiv2018

Automated leg tracking reveals distinct conserved gait and tremor signatures in Drosophila models of Parkinson’s Disease and Spinocerebellar ataxia 3

Genetic models in Drosophila have made invaluable contributions to our understanding of the molecular mechanisms underlying neurodegeneration. In human patients, some neurodegenerative diseases lead to characteristic movement dysfunctions, such as abnormal gait and tremors. However, it is currently unknown whether similar movement defects occur in the respective fly models, which could be used to model and better understand the pathophysiology of movement disorders. To address this question, we developed a machine-learning image-analysis programme -- Feature Learning-based LImb segmentation and Tracking (FLLIT) -- that automatically tracks leg claw positions of freely moving flies recorded on high-speed video, generating a series of body and leg movement parameters. Of note, FLLIT requires no user input for learning. We used FLLIT to characterise fly models of Parkinsons Disease (PD) and Spinocerebellar ataxia 3 (SCA3). Between these models, walking gait and tremor characteristics differed markedly, and recapitulated signatures of the respective human diseases. Selective expression of mutant SCA3 in dopaminergic neurons led to phenotypes resembling that of PD flies, suggesting that the behavioural phenotype may depend on the circuits affected, rather than the specific nature of the mutation. Different mutations produced tremors in distinct leg pairs, indicating that different motor circuits are affected. Almost 190,000 video frames were tracked in this study, allowing, for the first time, high-throughput analysis of gait and tremor features in Drosophila mutants. As an efficient assay of mutant gait and tremor features in an important model system, FLLIT will enable the analysis of the neurogenetic mechanisms that underlie movement disorders.

neuroscience↗

bioRxiv2018

Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera

Recent theory posits that adaptive evolution of reproductive proteins should depend on rates of female remating. In particular, selection on reproductive proteins is proposed to be weak unless females remate frequently, in which case cryptic female choice and sperm competition impose stronger selection. Here, we test these predictions by explicitly examining the role of selection in the molecular evolution of sperm genes in Lepidoptera, the butterflies and moths. Males of this order produce both fertilizing eupyrene sperm and a secondary apyrene type that lacks DNA. Based on population genetic analyses in two species, the monandrous Carolina sphinx moth and the highly polyandrous monarch butterfly, we see evidence for increased selection in fertilizing sperm, but only in the polyandrous species. This signal comes primarily from a decrease in non-synonymous polymorphism in sperm proteins compared to the rest of the genome, indicative of strong purifying selection. Investigation of the distribution of fitness effects of new non-synonymous mutations in monarch sperm confirms stronger selection on sperm proteins in monarchs, with very few neutral variants and weakly deleterious variants and a preponderance of strongly deleterious variants. Additionally, sperm genes in the monarch show an elevation of beneficial variants compared to the rest of the genome, suggesting a role for increased positive selection. Our results suggest that sperm competition can be a powerful selective force at the sequence level as well.

evolutionary biology↗

bioRxiv2018

Hydroxymethylated-P16 Allele Is Transcription-Inactive

Background5-Methylcytosine can be oxidized into 5-hydroxymethylcytosine (5hmC) in the genome. Methylated-P16 (P16M) can be oxidized into completely hydroxymethylated-P16 (P16H) in human cancer and precancer cells. The aim of this study is to investigate the biological function of P16H.\n\nMethodsTrue P16M and P16H were analyzed using bisulfite/TAB-based assays. A ZFP-based P16-specific dioxygenase (P16-TET) was constructed and used to induce P16H. Cell proliferation and migration were determined with a series of biological analyses.\n\nResults(A) The 5hmCs were enriched in the antisense-strand of the P16 exon-1 in HCT116 and AGS cells containing methylated-P16 alleles (P16M). (B) P16-TET induced both P16H and P16 demethylation in H1299 and AGS cells and reactivated P16 expression. Notably, P16H was only detectable in the sorted P16-TET H1299 and AGS cells that did not show P16 expression. (C) P16-TET significantly inhibited the xenograft growth derived from H1299 cells in NOD-SCID mice, but did not inhibit the growth of P16-deleted A549 control cells. P16-siRNA knockdown could rescue P16-TET-inhibited cell migration.\n\nConclusionHydroxymethylated P16 alleles are transcriptionally inactive.\n\nAUTHOR SUMMARYIt is well known that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidations, a certain proportion of 5hmCs remain in the genome. Although it is supposed that occurrence of 5hmCs may contribute to the flexibility of chromatin and the protection of the bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In the present study, we engineered a zinc-finger protein-based P16-specific DNA dioxygenase and used it to induce P16 hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that the hydroxymethylated P16 alleles retain transcriptionally inactive. This is supported by our recent findings that mRNAs are always transcribed only from the unmethylated P16 strands, but not from the hydroxymethylated/methylated strands in HCT116 cells, and that the risks for malignant transformation are similar for patients with the P16 methylation-positive oral epithelial dysplasia with and without P16 hydroxymethylation in a prospective study.

molecular biology↗

bioRxiv2018

The expansion of apolipoprotein D genes in cluster in teleost fishes

BackgroundGene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attentions considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the ligand (e.g., pheromone and hormone)-transporter genes, apolipoprotein D (ApoD) genes in a cluster, specific to teleost fishes.\n\nResultsThe single ApoD gene in the ancestor expands in two clusters with a dynamic evolutionary pattern in teleost fishes. Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, evolutionary rate detection and breakpoint detection, orthologous genes show conserved expression patterns. Lineage-specific duplicated genes that are under positive selection evolved specific and even new expression profiles. Different duplicates show high tissue-specific expression patterns (e.g., skin, eye, anal fin pigmentation patterns, gonads, gills, spleen and lower pharyngeal jaw). Cluster analyses based on protein 3D structure comparisons, especially the four loops at the opening side, show segregation patterns with different duplicates. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes, and they are located next to the breakpoints of genome rearrangements.\n\nConclusionsHere, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both protein and expression levels after duplication. Evidence from different aspects, i.e. abnormal expression induced disease in human, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, highly specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes that are under positive selection, and their locations next to breakpoints of genome rearrangement, suggests the potential advantageous roles of ApoD genes in teleost fishes. Cluster expansion of ApoD genes specific to teleost fishes thus provides an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.

evolutionary biology↗

bioRxiv2017

Revelation of the Genetic Basis for Convergent Innovative Anal Fin Pigmentation Patterns in Cichlid Fishes

Determining whether convergent novelties share a common genetic basis is vital to understanding the extent to which evolution is predictable. The convergent evolution of innovative anal fin pigmentation patterns in cichlid fishes is an ideal model for studying this question. Here, we focused on two patterns: 1) egg-spots, circular pigmentation patterns with different numbers, sizes and positions; and 2) the blotch, irregular pattern with no variation among species. How these two novelties originate and evolve remains unclear. Based on a thorough comparative transcriptomic and genomic analysis, we observed a common genetic basis with high evolutionary rates and similar expression levels between egg-spots and the blotch. Furthermore, associations of common genes with transcription factors and signalling pathways in the core gene network, as well as the integration of advantageous genes were observed for egg-spots. We propose that the re-use of the common genetic basis indicates important conservative functions (e.g., toolkit genes) for the origin of these convergent novel phenotypes, whereas independently evolved associations of common genes with transcription factors and signalling pathways (intrinsic factor) can free the evolution of egg-spots, and together with the integration of advantageous genes (extrinsic factor) can provide a clue to link egg-spots as a key innovation to the adaptive radiation in cichlid fishes. This hypothesis will further illuminate the mechanism of the origin and evolution of novelties in a broad sense.

evolutionary biology↗