Multiple Sequence Analysis Research Articles

PatchProt: Hydrophobic patch prediction using protein foundation models

Abstract Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed hydrophobic patches from a protein sequence has shown to be a difficult task. Fine-tuning foundation models allows for adapting a model to the specific nuances of a new task using a much smaller dataset. Additionally, multi-task deep learning offers a promising solution for addressing data gaps, simultaneously outperforming single-task methods. In this study, we harnessed a recently released leading large language model ESM-2. Efficient fine-tuning of ESM-2 was achieved by leveraging a recently developed parameter-efficient fine-tuning method. This approach enabled comprehensive training of model layers without excessive parameters and without the need to include a computationally expensive multiple sequence analysis. We explored several related tasks, at local (residue) and global (protein) levels, to improve the representation of the model. As a result, our model, PatchProt, cannot only predict hydrophobic patch areas but also outperforms existing methods at predicting primary tasks, including secondary structure and surface accessibility predictions. Importantly, our analysis shows that including related local tasks can improve predictions on more difficult global tasks. This research sets a new standard for sequence-based protein property prediction and highlights the remarkable potential of fine-tuning foundation models enriching the model representation by training over related tasks. Availability and implementation https://github.com/Deagogishvili/chapter-multi-task

Unearthing Optimal Symbiotic Rhizobia Partners from the Main Production Area of Phaseolus vulgaris in Yunnan.

Phaseolus vulgaris is a globally important legume cash crop, which can carry out symbiotic nitrogen fixation with rhizobia. The presence of suitable rhizobia in cultivating soils is crucial for legume cropping, especially in areas beyond the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with P. vulgaris in soils of Yunnan, where the common bean experienced a recent expansion. A total of 608 rhizobial isolates were tracked from soils of fifteen sampling sites using two local varieties of P. vulgaris. The isolates were discriminated into 43 genotypes as defined by IGS PCR-RFLP. Multiple locus sequence analysis based on recA, atpD and rpoB of representative strains placed them into 11 rhizobial species of Rhizobium involving Rhizobium sophorae, Rhizobium acidisoli, Rhizobium ecuadorense, Rhizobium hidalgonense, Rhizobium vallis, Rhizobium sophoriradicis, Rhizobium croatiense, Rhizobium anhuiense, Rhizobium phaseoli, Rhizobium chutanense and Rhizobium etli, and five unknown Rhizobium species; Rhizobium genosp. I~V. R. phaseoli and R. anhuiense were the dominant species (28.0% and 28.8%) most widely distributed, followed by R. croatiense (14.8%). The other rhizobial species were less numerous or site-specific. Phylogenies of nodC and nifH markers, were divided into two specific symbiovars, sv. phaseoli regardless of the species affiliation and sv. viciae associated with R. vallis. Through symbiotic effect assessment, all the tested strains nodulated both P. vulgaris varieties, often resulting with a significant greenness index (91-98%). However, about half of them exhibited better plant biomass performance, at least on one common bean variety, and two isolates (CYAH-6 and BLYH-15) showed a better symbiotic efficiency score. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature, drought and glyphosate. One strain efficient on both varieties and exhibiting stress abiotic tolerance (BLYH-15) belonged to R. genosp. IV sv. phaseoli, a species first found as a legume symbiont.

CcPTGS2a-like gene-mediated NF-κB/ERK signaling regulation in the common carp (Cyprinus carpio)

Prostaglandin-endoperoxide synthase 2 (PTGS2), a common biological macromolecule, is pivotal for innate immunity and pathogen recognition. In this study, we identified and characterized a CcPTGS2a-like gene in the common carp (Cyprinus carpio) with an open reading frame (ORF) of 1821 bp and epidermal growth factor and peroxidase domains. Our multiple sequence analysis revealed high homology between the amino acid sequence of CcPTGS2a-like and those of its homologs in other fish. CcPTGS2a-like mRNA and protein expressions were significantly upregulated in the spleen, head kidney, liver, and gill tissues upon exposure to Aeromonas hydrophila stimulation. CcPTGS2a-like protein recognized the conserved bacterial surface components and exhibited detectable bacterial binding activity. CcPTGS2a-like overexpression before exposure to A. hydrophila notably enhanced the survival rate of common carp, concomitant with decreased bacterial burden. The NF-κB/ERK signaling pathway initiated the immune response in common carp upon infection with A. hydrophila. CcPTGS2a-like overexpression or interference in the head kidney and Epithelioma papulosum cyprinid cells could modulate the p–NF–κB (p-p-65), p-IκBα, and p-ERK1/2 levels as well as the IL-1β and IL-6 mRNA expression. These results indicated potential CcPTGS2a-like involvement in the immune response of the common carp to bacterial infections through the NF-κB/ERK signaling pathway.

Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer.

Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.

Rhizobium acaciae and R. anhuiense are the dominant rhizobial symbionts of Pisum sativum L. from Yunnan-Guizhou Plateau.

The aim of this study is to investigate the diversity and geographic distribution of pea-nodulating rhizobia in the subtropical region of Yunnan Province from Yunnan-Guizhou Plateau. A total of 615 rhizobial isolates were obtained from root nodules of the trapping plants and characterized genetically and symbiotically. The isolates discriminated into 43 genotypes by PCR-RFLP of IGS DNA. Multiple locus sequence analysis based on 16S rRNA, recA, atpD, dnaK, and rpoB genes placed them into eight clusters corresponding to species R. acaciae, R. anhuiense, R. binae, R. bangladeshense, R. hidalgonense, and three suspected novel populations of Rhizobium genosp. I-III. R. acaciae was the dominant group (52.5%) followed by R. anhuiense (30.7%). The other species were minor groups. Based on nodC phylogeny, all of them were the symbiovar viciae. All the tested strains showed efficient symbiotic N2 fixation on pea plants, in which WLB27, WCB18, and WNY29 presented the best PGP effects. Some of the tested strains had better IAA production, with WCB18 as the best producer (64.556 mg/L). Their distribution was mainly affected by soil available phosphorus, available potassium, and effective nitrogen. According to the results of symbiotic effect and resistance tests, strains of WLB27, WCB18, and WNY29 were selected as candidates for creating inoculants. This suggests that the pea-nodulating rhizobia in Yunnan Province form a unique community. The results gave some novel information about the diversity, diversification, and biogeography of pea-nodulating rhizobia.

In silico Analysis of Anti-cervical Cancer Drug Off-Target Effects on Diverse Protein Isoforms for Enhanced Therapeutic Strategies

Background. Cervical cancer is a serious medical condition that affects hundreds of thousands of individuals worldwide annually. The selection and analysis of suitable gene targets in the early stages of drug design are crucial for combating this disease. However, overlooking the presence of various protein isoforms may result in unwanted therapeutic or harmful side effects. Objective. This study aimed to provide a computational analysis of the interactions between cervical cancer drugs and their targets, influenced by alternative splicing. Methods. Using open-access databases, we targeted 45 FDA-approved cervical cancer drugs that target various genes having more than two distinct protein-coding isoforms. To check the conservation of binding pocket in isoforms of the genes, multiple sequence analysis was performed. To better understand the associations between proteins and FDA-approved drugs at the isoform level, we conducted molecular docking analysis. Results. The study reveals that many drugs lack potential targets at the isoform level. Further examination of various isoforms of the same gene revealed distinct ligand-binding pocket configurations, including differences in size, shape, electrostatic characteristics, and structure. Conclusions. This study highlights the potential risks of focusing solely on the canonical isoform, and ignoring the impact of cervical cancer drugs on- and off-target effects at the isoform level. These findings emphasize the importance of considering interactions between drugs and their targets at the isoform level to promote effective treatment outcomes.

Analysis of Multiple PCR Bands in Drimia Species Obtained by R-Gene Specific Degenerate Primers

Many studies confirmed that degenerate primers LM638 and LM637 amplify NBS-LRR Type R gene encoding sequences in both monocots and dicots. In addition, these primers also amplify nonspecific multiple bands along with specific amplification. The current study aims to explore the structure, role and reason for nonspecific bands in the amplification. The genomic DNA-degenerate PCR method was used to isolate the NBS-LRR type R-genes in Drimia species (synonym Urginea). Agarose gel electrophoresis was carried out for separation and visualization of amplified bands. The kit-based gel extraction method was followed to purify the PCR bands. Purified PCR bands were subjected to TA cloning. The plasmids which contain desired PCR bands were sequenced using the Sanger sequencing method. Multiple sequence alignment tool CLUSTALW was used to align sequences and MISA-Web tool was used to identify simple sequence repeats (SSR). The results of the study revealed that multiple sequence analysis of PCR bands of 600bp/500bp showed random deletions, presence of indels and frameshift mutations in the alignment. The sequence alignment also showed monomorphic sites between two sequences. Both 600 and 500bp were devoid of simple sequence repeats and the ORF finder confirmed the presence of irregular stop codons in the 600 bp sequences. The multiple sequence alignment tool was used in disclosing the structure and ancestor relationship between aligned Drimia sequences. The current study would help to explore pseudo genes in the genome of Drimia and to differentiate the orthologous and paralogous relationships in the sequences.

Signal Classification in Large-Scale Multi-Sequence Integrative Analysis Under the HMM Dependence

The integrative analysis of multiple sequences of multiple tests has enjoyed increasing popularity in many applications, especially in large-scale genomics. In the context of large-scale multiple testing, the concept of signal classification has been developed recently for cases when the same features are involved in several independent studies, with the goal of classifying each feature into one of several classes. This article considers the problem of such signal classification in a generalized compound decision-making framework, where the observed data are assumed to be generated from an underlying four-state Cartesian hidden Markov model. Two oracle procedures are proposed for the total and set-specific control of misclassification rates, respectively, while the number of correct classifications is maximized. Optimal data-driven procedures are also proposed, with their asymptotic properties derived. It is shown that signal-classification could be improved significantly by taking into account the dependence structure among features, and the proposed procedures could have a better performance than their competitors that ignore the dependence structure. The proposed methods are applied to a psychiatric genetics study for detecting genetic variants that affect either or both of bipolar disorder and schizophrenia.

Acaricides resistance in Rhipicephalus microplus and expression profile of ABC-transporter genes in the sampled populations

Currently, livestock owners manage tick infestations using chemicals, but the method is increasingly losing effectiveness as resistant tick populations have established in the field conditions. Thus, to develop effective tick management strategies, monitoring of resistance in most predominant tick species, Rhipicephalus microplus was targeted. The ticks were collected from eleven districts of Madhya Pradesh and one district of Punjab and tested against deltamethrin (DLM), cypermethrin (CYP), coumaphos (CMP), ivermectin (IVM) and fipronil (FIP), through adult immersion and larval packet tests. The field isolates were highly resistant to DLM [Resistance factor (RF) = 3.98–38.84]. Against CYP, resistance was observed in BWN (Barwani; RF = 2.81) and MND (Mandsaur; RF = 3.23) isolates. Surprisingly, most of the isolates were susceptible to CMP (0.34–1.58). Emerging level of resistance against IVM (1.05–4.98) and FIP (0.40–2.18) was also observed in all the isolates. Significantly elevated production of esterases (p < 0.01) was 90% correlated with RF of DLM while no positive correlation between production of monooxygenase and Glutathione S-transferase with RF to DLM was noted. Multiple sequence analysis of S4-5 linker region of the sodium channel gene of all the isolates revealed a point mutation at 190th position (C190A) which is associated with DLM resistance. Treatment of resistant LDH (Ludhiana) isolate with IVM resulted in upregulation of RmABCC2 gene and insignificant upregulation of RmABCC1 and RmABCB10 genes indicating the probability of linking IVM resistance with over-expression of RmABCC2 gene. The possible tick management strategies are discussed.

Genotypic composition and performance of pea-nodulating rhizobia from soils outside the native plant-host range.

Cultivated soils need to shelter suitable rhizobia for legume cropping, especially in areas outside of the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with Pisum sativum L. in soils of Hebei Province, a region that has recently experienced an expansion of pea production in China. A total of 43 rhizobial isolates were obtained from root-nodules and characterized genetically and symbiotically. The isolates discriminated into 12 genotypes as defined by PCR-RFLP of IGS DNA. Multiple locus sequence analysis (MLSA) based on the 16S rRNA, recA, atpD and gyrB of representative strains placed them into five clusters of four defined species (R. sophorae, R. indicum, R. changzhiense, and R. anhuiense) and a novel Rhizobium genospecies. R. sophorae was the dominant group (58%) followed by R. indicum (23%). The other groups composed of R. changzhiense (14%), R. anhuiense (1 isolate) and the new genospecies (1 isolate), were minor and site-specific. Based on nodC phylogeny, all representatives were intermingled within the symbiovar viciae with R. sophorae and R. changzhiense being a new record. All the tested strains showed efficient symbiotic fixation on pea plants, with half of them exhibiting better plant biomass performance. This suggests that the pea-nodulating rhizobia in Hebei Province form a specific community of efficient symbiotic rhizobia on pea, distinct from those reported in other countries.

In silico analysis of potential loci for the identification of Vanda spp. in the Philippines

Difficulties in identifying Vanda species are still encountered, and the ambiguity in its taxonomy is still unresolved. To date, the advancement in molecular genetics technology has given rise to the molecular method for plant identification and elucidation. One hundred twenty-five (125) gene sequences of Vanda species from the Philippines were obtained from the NCBI GenBank. Four of the 25 loci were further examined using MEGA 11 software for multiple sequence alignment, sequence analysis, and phylogenetic reconstruction. The indel-based and tree-based methods were combined to compute the species resolution. The result showed that ITS from the nuclear region obtained the highest species resolution with 66.67%. It was then followed by psbA-trnH, matK, and trnL-trnF from the chloroplast genome with a species resolution of 60%, 40%, and 30.77%, respectively. ITS and psbA-trnH satisfied the ideal length for DNA barcoding as they have 655 bp and 701 bp, respectively. The locus psbA-trnH was also considered to have a higher potential to discriminate Vanda species since only a few sequences were tested for ITS. Furthermore, ITS and trnL-trnF have the highest variable rate, which is 2.9%, while matK and psbA-trnH have 2% and 1.3%, respectively. This showed the nature of the unique sequences of various species. In this study, the indel-based method provided better results than the tree-based method. It will help support further DNA barcoding studies and strengthen the conservation and protection of Vanda spp. in the Philippines.

Ensifer canadensis sp. nov. strain T173T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae.

A bacterial strain, designated T173T, was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173T was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173T. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173T in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04T as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173T compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173T has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173T. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173T. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173T (= LMG 32374T = HAMBI 3766T) as the species type strain.

Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin (Citrus reticulata)

WRKY proteins are an important group of transcription factors (TFs) gene family and were identified primarily in plants. WRKY TFs play vital roles in modulating gene expression when plants face detrimental effects due to the environment. In the current study, we focused on using the mandarin citrus (Citrus reticulata) genome to understand the impact of the WRKY gene family on the extraction of alleles mining in mandarins. The mining of the C. reticulata genome identified 46 CrWRKY genes that were classified into three main groups (G1, G2, and G3) further with five subclasses (IIa, IIb, IIc, Iid, and IIe) in the G2 group, and all were presented on 29 scaffolds representing numerous segmental duplications of 100% events established. Multiple sequence analysis predicted the presence of the “WRKYGQK” domain and metal-chelating zinc-finger motif C2H2 in 45 genes, while the “WRKYGQK” domain was replaced with “WRKYGKK” only in CrWRKY20. The comparative relationship of CrWRKY with other plant species using dual synteny analysis revealed that the divergence between C. reticulata and C. grandis occurred after the evolutionary divergence of C. clementine, C. sinensis, C. medica, and C. ichangensis. The possible functions of the CrWRKY genes in mitigating environmental effects were predicted using cis-regulatory elements analysis and in silico RNAseq analysis, for the development of plants. These results provide a robust platform and absence of knowledge for the functional identification from key genes of CrWRKY genes in the mandarin for the possible use to improve key desirable agronomic and consumer-driven fruit quality traits in mandarins and related species.

Seismic resilience assessment of Small Modular Reactors by a Three-loop Monte Carlo Simulation

We develop a three-loop Monte Carlo Simulation (MCS) framework for the seismic resilience assessment of Small Modular Reactors (SMRs), embedding Probabilistic Seismic Hazard Analysis (PSHA), seismic fragility evaluation and multiple SMR units accident sequence analysis. A set of metrics are computed to capture different aspects of SMR resilience to earthquakes, specifically the ability to withstand seismic disruption, mitigate consequences and restore normal operation. The MCS framework allows accounting for the aleatory and epistemic uncertainties of the PSHA and fragility parameters. An application is given with regards to an advanced Nuclear Power Plant (aNPP) consisting of four reactor units of NuScale SMR design. A comparison is made to a conventional NPP (cNPP), i.e., a typical large reactor of equivalent generation capacity. Both plants are fictitiously located on the Garigliano nuclear site (southern Italy). The results show that resilient features of SMRs overcome cNPPs in terms of post-accident scenario mitigation and restoration capabilities.

Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum).

YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.

Molecular characterization and functional analysis of CD209E from Nile Tilapia (Oreochromis Niloticus) involved in immune response to bacterial infection

CD209 plays significant roles in pathogen recognition, innate and adaptive immunity, and cell-cell interactions. In the present study, a CD209 antigen-like protein E from Nile tilapia (Oreochromis niloticus) (designated as OnCD209E) was identified and characterized. OnCD209E contains an open reading frame (ORF) of 771 bp encoding a 257 amino acid protein, as well as the carbohydrate recognition domain (CRD). Multiple sequence analysis exhibits that the amino acid sequence of OnCD209E was relatively high homologous to that of partial fish, especially the highly conserved CRD, in which four conserved disulfide-bonded cysteine residues, WIGL conserved motif and two Ca2+/carbohydrate-binding sites (EPD and WFD motifs) were founded. Quantitative real-time PCR and Western Blot revealed that OnCD209E mRNA/protein is generally expressed in all tissues examined, but with wealth in head kidney and spleen tissues. The mRNA expression of OnCD209E was significantly increased in brain, head kidney, intestine, liver, and spleen tissues in response to the stimulation with polyinosinic-polycytidylic acid, Streptococcus agalactiae and Aeromonas hydrophila in vitro. Recombinant OnCD209E protein exhibited detectable bacterial binding and agglutination activity against different bacteria as well as inhibited the proliferation of tested bacteria. Subcellular localization analysis revealed that OnCD209E was mostly localized in the cell membrane. Moreover, overexpression of OnCD209E could activate nuclear factor-kappa B reporter genes in HEK-293T cells. Collectively, these results demonstrated that CD209E may potentially involve in immune response of Nile tilapia against bacterial infection.

Comprehensive Analysis of BR Receptor Expression under Hormone Treatment in the Rubber Tree (Hevea brasiliensis Muell. Arg.).

Brassinosteroids (BRs) are important for plant growth and development, with BRI1 and BAK1 kinases playing an important role in BR signal transduction. Latex from rubber trees is crucial for industry, medicine and defense use. Therefore, it is beneficial to characterize and analyze HbBRI1 and HbBAK1 genes to improve the quality of the resources obtained from Hevea brasiliensis (rubber tree). Based on bioinformatics predictions and rubber tree database, five HbBRI1s with four HbBAK1s were identified and named HbBRI1~HbBRL3 and HbBAK1a~HbBAK1d, respectively, which were clustered in two groups. HbBRI1 genes, except for HbBRL3, exclusively contain introns, which is convenient for responding to external factors, whereas HbBAK1b/c/d contain 10 introns and 11 exons, and HbBAK1a contains eight introns. Multiple sequence analysis showed that HbBRI1s include typical domains of the BRI1 kinase, indicating that HbBRI1s belong to BRI1. HbBAK1s that possess LRR and STK_BAK1_like domains illustrate that HbBAK1s belong to the BAK1 kinase. BRI1 and BAK1 play an important role in regulating plant hormone signal transduction. Analysis of the cis-element of all HbBRI1 and HbBAK1 genes identified hormone response, light regulation and abiotic stress elements in the promoters of HbBRI1s and HbBAK1s. The results of tissue expression patterns indicate that HbBRL1/2/3/4 and HbBAK1a/b/c are highly expressed in the flower, especially HbBRL2-1. The expression of HbBRL3 is extremely high in the stem, and the expression of HbBAK1d is extremely high in the root. Expression profiles with different hormones show that HbBRI1 and HbBAK1 genes are extremely induced by different hormone stimulates. These results provide theoretical foundations for further research on the functions of BR receptors, especially in response to hormone signals in the rubber tree.

In Silico Exploration of Microtubule Agent Griseofulvin and Its Derivatives Interactions with Different Human β-Tubulin Isotypes

Tubulin isotypes are known to regulate microtubule stability and dynamics, as well as to play a role in the development of resistance to microtubule-targeted cancer drugs. Griseofulvin is known to disrupt cell microtubule dynamics and cause cell death in cancer cells through binding to tubulin protein at the taxol site. However, the detailed binding mode involved molecular interactions, and binding affinities with different human β-tubulin isotypes are not well understood. Here, the binding affinities of human β-tubulin isotypes with griseofulvin and its derivatives were investigated using molecular docking, molecular dynamics simulation, and binding energy calculations. Multiple sequence analysis shows that the amino acid sequences are different in the griseofulvin binding pocket of βI isotypes. However, no differences were observed at the griseofulvin binding pocket of other β-tubulin isotypes. Our molecular docking results show the favorable interaction and significant affinity of griseofulvin and its derivatives toward human β-tubulin isotypes. Further, molecular dynamics simulation results show the structural stability of most β-tubulin isotypes upon binding to the G1 derivative. Taxol is an effective drug in breast cancer, but resistance to it is known. Modern anticancer treatments use a combination of multiple drugs to alleviate the problem of cancer cells resistance to chemotherapy. Our study provides a significant understanding of the involved molecular interactions of griseofulvin and its derivatives with β-tubulin isotypes, which may help to design potent griseofulvin analogues for specific tubulin isotypes in multidrug-resistance cancer cells in future.

Mucormycosis-causing fungi in humans: a meta-analysis establishing the phylogenetic relationships using internal transcribed spacer (ITS) sequences.

Introduction. Mucormycosis is a severe angio-invasive fungal infection caused by mucormycetes, a group of fungi that are ubiquitous in the environment. The incidence of mucormycosis has been surging rapidly due to the global corona virus disease 2019 (COVID-19) pandemic.Gap Statement. The complete picture of the causative fungi associated with mucormycosis and their phylogenetic relationships are not well defined.Aim. This meta-analysis aimed to collate all confirmed fungal pathogens that cause mucormycosis, and assess their taxonomic relationships.Methodology. All types of articles in the PubMed database that report fungi as a cause of mucormycosis were reviewed. We summarized the fungal morphological characteristic up to the genus level. The internal transcribed spacer (ITS) nucleotide sequences of these fungi were retrieved from the National Center for Biotechnology Information (NCBI) and UNITE databases whenever available, and multiple sequence analysis was conducted using Clustal W. The phylogenetic tree was constructed using mega version 7.Results. Forty-seven fungal species were identified as pathogens causing mucormycosis in humans. Thirty-two fungal species were phylogenetically grouped into three clades, and it was evident that the ITS sequences have well-conserved regions in all clades, especially from the 400th to 500th base pairs.Conclusion. The findings of this work contribute to the descriptive data for fungi that cause mucormycosis, emphasizing the need for robust phylogenetic approaches when identifying clinical isolates from infected patients.

The protein family of pyruvate:quinone oxidoreductases: Amino acid sequence conservation and taxonomic distribution

Pyruvate:quinone oxidoreductases (PQOs) catalyse the oxidative decarboxylation of pyruvate to acetate and concomitant reduction of quinone to quinol with the release of CO2. They are thiamine pyrophosphate (TPP) and flavin-adenine dinucleotide (FAD) containing enzymes, which interact with the membrane in a monotopic way. PQOs are considered as part of alternatives to most recognized pyruvate catabolizing pathways, and little is known about their taxonomic distribution and structural/functional relationship.In this bioinformatics work we tackled these gaps in PQO knowledge. We used the KEGG database to identify PQO coding genes, performed a multiple sequence analysis which allowed us to study the amino acid conservation on these enzymes, and looked at their possible cellular function. We observed that PQOS are enzymes exclusively present in prokaryotes with most of the sequences identified in bacteria. Regarding the amino acid sequence conservation, we found that 75 amino acid residues (out of 570, on average) have a conservation over 90 %, and that the most conserved regions in the protein are observed around the TPP and FAD binding sites. We systematized the presence of conserved features involved in Mg2+, TPP and FAD binding, as well as residues directly linked to the catalytic mechanism. We also established the presence of a new motif named “HEH lock”, possibly involved in the dimerization process. The results here obtained for the PQO protein family contribute to a better understanding of the biochemistry of these respiratory enzymes.