Comprehensive identification and systematical characterization of BRX gene family and the functional of GhBRXL5A in response to salt stress.

BACKGROUND: BRVIS RADIX (BRX) family is a small gene family with the highly conserved plant-specific BRX domains, which plays important roles in plant development and response to abiotic stress. Although BRX protein has been studied in other plants, the biological function of cotton BRX-like (BRXL) gene family is still elusive. RESULT: In this study, a total of 36 BRXL genes were identified in four cotton species. Whole genome or segmental duplications played the main role in the expansion of GhBRXL gene family during evolutionary process in cotton. These BRXL genes were clustered into 2 groups, α and ß, in which structural and functional conservation within same groups but divergence among different groups were found. Promoter analysis indicated that cis-elements were associated with the phytohormone regulatory networks and the response to abiotic stress. Transcriptomic analysis indicated that GhBRXL2A/2D and GhBRXL5A/5D were up/down-regulated in response to the different stress. Silencing of GhBRXL5A gene via virus-induced gene silencing (VIGS) improved salt tolerance in cotton plants. Furthermore, yeast two hybrid analysis suggested homotypic and heterotypic interactions between GhBRXL1A and GhBRXL5D. CONCLUSIONS: Overall, these results provide useful and valuable information for understanding the evolution of cotton GhBRXL genes and their functions in salt stress.

Characteristic of GEX1 genes reveals the essential roles for reproduction in cotton.

GEX1 (gamete expressed 1) proteins are critical membrane proteins conserved among flowering plants that are involved in the nuclear fusion and embryonic development. Herein, we identified the 32 GEX1 proteins from representative land plants. In cotton, GEX1 genes expressed in various tissues across all stages of the life cycle, especially in pollen. Subcellular localization indicated the position of GhGEX1 protein was localized in the endoplasmic reticulum. Experimental research has demonstrated that GhGEX1 has the potential to improve the partial abortion phenotype in Arabidopsis. CRISPR/Cas9-mediated knockout of GhGEX1 exhibited the seed abortion. Paraffin section of the ovule revealed that the polar nuclear fusion of ghgex1 plants remains at a standstill when the wild type has developed into a normal embryo. Comparative transcriptome analysis showed that the DEGs of reproductive-related processes and membrane-related processes were repressed in the pollen of knockout lines. The predicted protein interactions showed that GhGEX1 probably functioned through interactions with proteins related to reproduction and membrane. From all these investigations, it was possible to conclude that the GEX1 proteins are evolutionarily conserved in flowering plants and elucidated the pivotal roles during fertilization and early embryonic development in cotton.

Lipids and Terpenoids from the Deep-Sea Fungus Trichoderma lixii R22 and Their Antagonism against Two Wheat Pathogens.

Five new lipids, tricholixins A-E (1-5), and two known terpenoids, brasilane A (6) and harzianone A (7), were discovered from a deep-sea strain (R22) of the fungus Trichoderma lixii isolated from the cold seep sediments of the South China Sea. Their structures and relative configurations were identified by meticulous analysis of MS and IR as well as NMR data. The absolute configuration of 5 was ascertained by dimolybdenum-induced ECD data in particular. Compounds 1 and 2 represent the only two new butenolides from marine-derived Trichoderma, and they further add to the structural diversity of these molecules. Although 6 has been reported from a basidiomycete previously, it is the first brasilane aminoglycoside of Trichoderma origin. During the assay against wheat-pathogenic fungi, both 1 and 2 inhibited Fusarium graminearum with an MIC value of 25.0 µg/mL, and 6 suppressed Gaeumannomyces graminis with an MIC value of 12.5 µg/mL. Moreover, the three isolates also showed low toxicity to the brine shrimp Artemia salina.

New ophiobolin sesterterpenoid and drimane sesquiterpenoids from a marine-alga-derived fungus Aspergillus sp.

Further investigation of secondary metabolites of a marine-alga-derived fungus Aspergillus sp. RR-YLW-12 led to isolate one new ophiobolin-type sesterterpenoid (1), four new drimane-type sesquiterpenoids (2-5) and one natural occurring compound (6), together with seven known compounds (7-13). Their structures and stereochemistry were elucidated by extensive spectroscopic analysis of NMR and HRMS experiments, and by comparison with the literature data. All isolates were evaluated for growth inhibition of five marine harmful microalgae. The new compounds exhibited significant to moderate inhibitory effects towards all tested microalgae species with IC50 values ranging from 5.8 to 54.5 µg/mL.

Myrochromanol analogues and trichothecene derivatives from the shellfish-derived fungus Albifimbriaverrucaria.

Eight myrochromanol analogues, including three pairs of epimers at C-2 with the myrochromanol scaffold and two examples of myrochromanol with sugar moiety linked at C-4, together with twelve trichothecene derivatives were isolated from the cultures of a shellfish-derived fungus Albifimbria verrucaria CD1-4. Among them, eight compounds named 2-epi-myrochromanol, ent-myrochromanol B, 4-epi-myrochromanol B, 2-epi-myrochromanol A, myrochromanosides A and B, 6',7'-erythro-(2'E,4'Z)-trichoverrol B, 3R,8S-dihyroxyroridin H were previously undescribed fungal metabolites. Their planar structures and relative configurations were established by 1D and 2D NMR, and HR-MS data analysis, and their absolute configurations were determined using the modified Mosher's method and electronic circular dichrosim calculations. Almost all isolates were evaluated for growth rate inhibition of three marine harmful microalgae Chattonella marina, Heterosigma akashiwo, and Prorocentrum donghaiense, and lethal activity to one marine zooplankton, Artemia salina. Myrochromanosides A and B exhibited obvious inhibitory against three tested microalgae with IC50 values in the range of 9.2-108.9 µM. 8α-Hydroxyroridin H, roridin A and verrucarin A exhibited significant inhibition against P. donghaiense with IC50 values of 6.1, 5.8, and 6.0 µM and toxicity against brine shrimp larvae with LC50 values of 1.4, 2.8, and 0.26 µM, respectively.

Alterbutenolide, a new butenolide derivative from a sponge-derived fungus Alternaria alternata I-YLW6-1.

Alterbutenolide (1), a new butenolide derivative with a long-chain aliphatic acid substitution, together with seven known phenolic compounds i.e. alternariol (2), asperigillol B (3), p-hydroxyphenylacetic acid (4), p-hydroxyphenylethyl alcohol (5), methyl p-hydroxyphenyl acetate (6), 2-(4-hydroxyphenyl)ethyl acetate (7), and 5,6-dihydro-4-methyl-2H-pyran-2-one (8), was isolated from the cultures of a sponge-derived fungus Alternaria alternata I-YLW6-1. The structure of 1 was established on the basis of HR-MS, 1D and 2D NMR, as well as by comparison of the optical rotation data with the literature reported. Compounds 2 and 3 showed significant to moderate inhibitory activities against three harmful microalgae with IC50 values from 3.0 to 36.2 µg/mL, whereas compound 1 only displayed moderate inhibition against Chattonella marina with IC50 value of 34.6 µg/mL. Meanwhile, compounds 3 and 4 showed weak toxicity against brine shrimp larvae with LC50 values >100 µg/mL.

A new lanostane-type triterpenoid from the marine shellfish symbiotic fungus Ceriporia lacerata CD7-5.

One new lanostane-type triterpenoid, 3ß-acetoxy-7,11-dioxolanosta-8,24-dien-21-oic acid (1), together with six known analogues (2-7), were isolated from the cultures of a marine fungus Ceriporia lacerata CD7-5, which was derived from the shellfish Ostrea denselamellosa. Their structures were determined by detailed analysis of spectroscopic data and comparison with the literature reported. The biological activities of these lanostane triterpenoids against marine-derived microalgae, zooplankton, and pathogenic bacteria were also evaluated in this study.

Identification, Classification and Characterization Analysis of FBXL Gene in Cotton.

F-box/LR (FBXL), Leucine-rich repeats in F-box proteins, belongs to the Skp1-Cullin1-F-box protein (SCF) E3 ligase family. FBXL genes play important roles in plant growth, such as plant hormones, responses to environmental stress, and floral organ development. Here, a total of 518 FBXL genes were identified and analyzed in six plant species. Phylogenetic analysis showed that AtFBXLs, VvFBXLs, and GrFBXLs were clustered into three subfamilies (Ⅰ-Ⅲ). Based on the composition of the F-box domain and carboxyl-terminal amino acid sequence, FBXL proteins were classified into three types (Type-A/-B/-C). Whole-genome duplication (WGD) along with tandem duplications and segmental contributed to the expansion of this gene family. The result indicates that four cotton species are also divided into three subfamilies. FBXLs in cotton were classified into three clades by phylogenetic and structural analyses. Furthermore, expression analyses indicated that the expression patterns of GhFBXLs in different cotton tissues were different. The highly expressed of GH_A07G2363 in 5-8 mm anthers, indicates that this gene might play a role in the reproductive process, providing candidate genes for future studies on cotton fertility materials. This study provides an original functional opinion and a useful interpretation of the FBXL protein family in cotton.

Systematical Characterization of the Cotton Di19 Gene Family and the Role of GhDi19-3 and GhDi19-4 as Two Negative Regulators in Response to Salt Stress.

Drought-induced 19 (Di19) protein is a Cys2/His2 (C2H2) type zinc-finger protein, which plays a crucial role in plant development and in response to abiotic stress. This study systematically investigated the characteristics of the GhDi19 gene family, including the member number, gene structure, chromosomal distribution, promoter cis-elements, and expression profiles. Transcriptomic analysis indicated that some GhDi19s were up-regulated under heat and salt stress. Particularly, two nuclear localized proteins, GhDi19-3 and GhDi19-4, were identified as being in potential salt stress responsive roles. GhDi19-3 and GhDi19-4 decreased sensitivity under salt stress through virus-induced gene silencing (VIGS), and showed significantly lower levels of H2O2, malondialdehyde (MDA), and peroxidase (POD) as well as significantly increased superoxide dismutase (SOD) activity. This suggested that their abilities were improved to effectively reduce the reactive oxygen species (ROS) damage. Furthermore, certain calcium signaling and abscisic acid (ABA)-responsive gene expression levels showed up- and down-regulation changes in target gene-silenced plants, suggesting that GhDi19-3 and GhDi19-4 were involved in calcium signaling and ABA signaling pathways in response to salt stress. In conclusion, GhDi19-3 and GhDi19-4, two negative transcription factors, were found to be responsive to salt stress through calcium signaling and ABA signaling pathways.

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton.

The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 JmjC genes (GhJMJs) were identified by genome-wide analysis in upland cotton (Gossypium hirsutum), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between G. hirsutum and Theobroma cacao. We have further explored the putative molecular regulatory mechanisms of the JmjC gene family in cotton. GhJMJ24 and GhJMJ49 were both preferentially expressed in embryogenic callus compared to nonembryogenic callus in cotton tissue culture, which might be regulated by transcription factors and microRNAs to some extent. Further experiments indicated that GhJMJ24 and GhJMJ49 might interact with SUVH4, SUVH6, DDM1, CMT3, and CMT1 in the nucleus, potentially in association with demethylation of H3K9me2. Taken together, our results provide a foundation for future research on the biological functions of GhJMJ genes in cotton, especially in somatic embryogenesis in cotton tissue culture, which is crucial for the regeneration of transgenic plants.

Terpenoids from the Marine-Derived Fungus Aspergillus sp. RR-YLW-12, Associated with the Red Alga Rhodomela confervoides.

Two new meroterpenoids, aspermeroterpenes D and E (1 and 2), two new ophiobolin-type sesterterpenoids, the C-18 epimers of 18,19-dihydro-18-methoxy-19-hydroxyophiobolin P (6 and 7), and two new drimane-type sesquiterpenoids, 3S-hydroxystrobilactone A (8) and 6-epi-strobilactone A (9), along with 11 known terpenoids (3-5 and 10-17) were isolated from the cultures of the algicolous fungus Aspergillus sp. RR-YLW-12, derived from the red alga Rhodomela confervoides. The structures and relative configurations of new compounds were established by detailed spectroscopic analysis of NMR and HRMS experiments, and the absolute configurations were assigned by X-ray diffraction experiments and comparison of their experimental and calculated ECD spectra. Compound 1 features a rare 6/6/6/6/5 pentacyclic system with a meroterpenoid skeleton, and the structure of terretonin E (3) was revised in this study. Compound 4 showed significant inhibitory activities against three microalgae, Prorocentrum donghaiense, Heterosigma akashiwo, and Chattonella marina, with IC50 values of 10.5, 5.2, and 3.1 µg/mL, respectively.

Cotton DMP gene family: characterization, evolution, and expression profiles during development and stress.

Members of DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (DMP) gene family, a type of plant-specific membrane proteins, have been proposed to function in various physiological processes such as reproductive development and senescence in plants. Here, a total of 174 DMP genes were identified and analyzed in 16 plant species (including 58 DMPs in four cotton species). Phylogenetic analysis showed that these DMPs could be clustered into five subfamilies (I-V). 137 duplicated cotton gene pairs were identified and most duplicate events were formed by whole-genome duplication (WGD)/segmental duplications. Expression analysis revealed that most of cotton DMPs were mainly expressed in the reproductive organs (the sepal, petal, pistil and anther) and the fiber of secondary cell wall stage. GhDMPs promoter regions containing the different cis-elements also showed different responses to abiotic stress. In addition, gene interaction networks showed that DMPs, as an endomembrane system, were involved in plant senescence process and flower reproductive development. We speculated GhDMP8-A/-D, GbDMP8-A/-D could be used as some candidate gene for inducing cotton haploid. This genome-wide study provides a systematic analysis of the cotton DMP gene family, and further insights towards understanding the potential functions of candidate genes.

Evolution and Functional Divergence of SUN Genes in Plants.

SUN-domain containing proteins are crucial nuclear membrane proteins involved in a plethora of biological functions, including meiosis, nuclear morphology, and embryonic development, but their evolutionary history and functional divergence are obscure. In all, 216 SUN proteins from protists, fungi, and plants were divided into two monophyletic clades (Cter-SUN and Mid-SUN). We performed comprehensive evolutionary analyses, investigating the characteristics of different subfamilies in plants. Mid-SUNs further evolved into two subgroups, SUN3 and SUN5, before the emergence of the ancestor of angiosperms, while Cter-SUNs retained one subfamily of SUN1. The two clades were distinct from each other in the conserved residues of the SUN domain, the TM motif, and exon/intron structures. The gene losses occurred with equal frequency between these two clades, but duplication events of Mid-SUNs were more frequent. In cotton, SUN3 proteins are primarily expressed in petals and stamens and are moderately expressed in other tissues, whereas SUN5 proteins are specifically expressed in mature pollen. Virus-induced knock-down and the CRISPR/Cas9-mediated knockout of GbSUN5 both showed higher ratios of aborted seeds, although pollen viability remained normal. Our results indicated divergence of biological function between SUN3 and SUN5, and that SUN5 plays an important role in reproductive development.

Phenylhydrazone and Quinazoline Derivatives from the Cold-Seep-Derived Fungus Penicillium oxalicum.

Three new phenylhydrazones, penoxahydrazones A-C (compounds 1-3), and two new quinazolines, penoxazolones A (compound 4) and B (compound 5), with unique linkages were isolated from the fungus Penicillium oxalicum obtained from the deep sea cold seep. Their structures and relative configurations were assigned by analysis of 1D/2D NMR and mass spectroscopic data, and the absolute configurations of 1, 4, and 5 were established on the basis of X-ray crystallography or ECD calculations. Compound 1 represents the first natural phenylhydrazone-bearing steroid, while compounds 2 and 3 are rarely occurring phenylhydrazone tautomers. Compounds 4 and 5 are enantiomers that feature quinazoline and cinnamic acid units. Some isolates exhibited inhibition of several marine phytoplankton species and marine-derived bacteria.

A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li3 of Tetraploid Cotton.

Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li3 was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li3 is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene's expression. The genetic loci n2 and n3 underlying the recessive fuzzless phenotype in Gossypium hirsutum were also mapped. The genomic location of n3 overlapped with that of the dominant fuzzless locus N1 , and n3 appeared to be a loss-of-function allele caused by a single nucleotide polymorphism (SNP) mutation in the coding region of GhMML3_A12. The n2 allele was found to be co-located with li3 and originated from G. babardense. n2 and li3 are possibly the multiple alleles of the GhMML3_D12 gene. Genetic analysis showed that Li3 and N3 are a pair of homologs with additive effects for the initiation of fibers (fuzz or lint). In addition, the presence of another locus was speculated, and it appeared to show an inhibitory effect on the expression of GhMML3. These findings provide new information about the genetic factors affecting the initiation of fibers in cotton.

Self-Sterilizing Polymeric Membrane Sensors Based on 6-Chloroindole Release for Prevention of Marine Biofouling.

A self-sterilizing strategy based on antimicrobial organic agent release is proposed for polymeric membrane sensors to prevent marine biofouling. A solid-contact polymeric membrane calcium ion-selective electrode (Ca2+-ISE) is selected as a model sensor. 6-Cholorindole (6-Cl indole) is utilized as the biocidal agent due to its potential antimicrobial activity and environmental friendliness. The plasticized polymeric membrane doped with 6-Cl indole shows a markedly improved antimicrobial activity against the bacterial cells collected from seawater and effectively prevents the formation of a biofilm on the sensor surface, while displaying response properties (i.e., linear range, selectivity, and response time) similar to those of the undoped membrane. Importantly, the present sensor can preserve an improved antimicrobial activity when kept in the artificial seawater for 45 days, indicating highly stable antibacterial properties of the membrane electrode. Additionally, the 6-Cl indole-doped Ca2+-ISE exhibits no significant loss of analytical performance after exposure to a rather concentrated bacterial suspension (∼109 colony-forming units per mL (CFU mL-1)) for 7 days. The proposed antimicrobial agent release methodology can be extended to develop polymeric membrane-based marine sensors with stable biofouling resistances against bacterial colonization.

Study on the optical and biological properties in vitro of IR808-PEG-FA.

IR808, an IR780 derivative, is capable of fluorescently imaging and photodynamic therapy in vitro and in vivo. However, its application is greatly hampered by hydrophobicity, toxicity and nonspecific delivery to the targeting tissue and that causes accumulation in the liver and kidney. In order to overcome these limitations, we prepared IR808-PEG-FA from IR808, amino-terminated poly(ethylene glycol) (NH2 -PEG-NH2 , denoted as PEG) and folate (FA). PEG, an accepted hydrophilic medicinal agent, was introduced to improve hydrophobicity, and FA was used to increase targeting ability of the conjugate. The obtained product provides a good water solubility and stronger light intensity in near infrared (NIR)-imaging, and CCK-8 test demonstrated which had no appreciable toxicity. In addition, the cell uptake results indicated that IR808-PEG-FA was specifically targeted to positive tumors cells with folate receptor (FR) compared with IR808, and thus it may be used as a novel diagnostic agent or imaging-guided agent for cancer treatment. So this article provides a way to improve hydrophobicity, optical stability and targeting ability in the field of nano-probe for fluorochromes.

Open-Bud Duplicate Loci Are Identified as MML10s, Orthologs of MIXTA-Like Genes on Homologous Chromosomes of Allotetraploid Cotton.

The open-bud (ob) mutants in cotton display abnormal flower buds with the stigma and upper anthers exposed before blooming. This characteristic is potentially useful for the efficient production of hybrid seeds. The recessive inheritance pattern of the ob phenotype in allotetraploid cotton is determined by duplicated recessive loci (ob1ob1ob2ob2). In this study, ob1, which is a MIXTA-like MYB gene on chromosome D13 (MML10_Dt), was identified by map-based cloning. In Gossypium barbadense (Gb) acc. 3-79, a single nucleotide polymorphism (SNP) (G/A) at the splice site of the first intron and an 8-bp deletion in the third exon of MML10_Dt were found, which are the causative mutations at the ob1 loci. A 1783-bp deletion that leads to the loss of the third exon and accounts for the causal variation at the ob2 loci was found in MML10_At of Gossypium hirsutum (Gh) acc. TM-1. The ob phenotype results from the combination of these two loss-of-function loci. Genotyping assays showed that the ob1 and ob2 loci appeared after the formation of allotetraploid cotton and were specific for Gb and Gh, respectively. All Gb lines and most Gh cultivars carry the single corresponding mutant alleles. Genome-wide transcriptome analysis showed that some of the MYB genes and genes related to cell wall biogenesis, trichome differentiation, cytokinin signal transduction, and cell division were repressed in the ob mutants, which may lead to suppression of petal growth. These findings should be of value for breeding superior ob lines in cotton.

Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium).

BACKGROUND: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. RESULTS: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the specific WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. CONCLUSION: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three types based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

Trichobisabolins A-H, eight new bisabolane derivatives from the marine-alga-epiphytic fungus Trichoderma asperellum Y6-2.

Eight new bisabolane derivatives, trichobisabolins A-H, along with two known ones, (3R,6R,7R)-1,10-bisaboladien-3-ol (9) and (3R,6R,7S)-1,10-bisaboladien-3,6-diol (10) were isolated from the culture of Trichoderma asperellum Y6-2, obtained from the surface of the marine red alga Chondrus ocellatus. Their structures and relative configurations were identified by interpretation of 1D/2D NMR and MS data. Compounds 1-8 were assayed for inhibiting the growth of some marine-derived organisms, including four marine phytoplankton species, one marine zooplankton species, and five pathogenic bacteria. All of them exhibited inhibition against the marine phytoplanktons with IC50 values ranging from 2.1-78 µg/mL, compounds 4 and 8 showed weak lethality to the marine zooplankton, and none of them had inhibition against the five pathogenic bacteria.