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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024; 931:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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Bertrans-Tubau L, Martínez-Campos S, Lopez-Doval J, Abril M, Ponsá S, Salvadó V, Hidalgo M, Pico-Tomàs A, Balcazar JL, Proia L. Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 22:100445. [PMID: 39055482 PMCID: PMC11269294 DOI: 10.1016/j.ese.2024.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.
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Affiliation(s)
- Lluís Bertrans-Tubau
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Martínez-Campos
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Julio Lopez-Doval
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Meritxell Abril
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Ponsá
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Victoria Salvadó
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Manuela Hidalgo
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Anna Pico-Tomàs
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
| | - Jose Luis Balcazar
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Lorenzo Proia
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
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3
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Abdelaziz MNS, Maung AT, El-Telbany M, Lwin SZC, Noor Mohammadi T, Zayda M, Wang C, Damaso CH, Lin Y, Masuda Y, Honjoh KI, Miyamoto T. Applications of bacteriophage in combination with nisin for controlling multidrug-resistant Bacillus cereus in broth and various food matrices. Food Res Int 2024; 191:114685. [PMID: 39059942 DOI: 10.1016/j.foodres.2024.114685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
This study focused on the isolation and characterization of bacteriophages with specific activity against toxin-producing and multidrug-resistant strains of Bacillus cereus sensu stricto (B. cereus s. s.). Ten different samples yielded six bacteriophages by utilizing the double-layer agar technique. The most promising phage, vB_BceS-M2, was selected based on its broad host range and robust lytic activity against various B. cereus s. s. strains. The phage vB_BceS-M2 had a circular double-stranded DNA genome of 56,482 bp. This phage exhibited stability over a wide range of temperatures and pH values, which is crucial for its potential application in food matrices. The combined effect of phage vB_BceS-M2 and nisin, a widely used antimicrobial peptide, was investigated to enhance antimicrobial efficacy against B. cereus in food. The results suggested that nisin showed synergy and combined effect with the phage, potentially overcoming the growth of phage-resistant bacteria in the broth. Furthermore, practical applications were conducted in various liquid and solid food matrices, including whole and skimmed milk, boiled rice, cheese, and frozen meatballs, both at 4 and 25 °C. Phage vB_BceS-M2, either alone or in combination with nisin, reduced the growth rate of B. cereus in foods other than whole milk. The combination of bacteriophage and nisin showed promise for the development of effective antimicrobial interventions to counteract toxigenic and antibiotic-resistant B. cereus in food.
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Affiliation(s)
- Marwa Nabil Sayed Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Food Hygiene, Animal Health Research Institute (AHRI), Agriculture Research Center (ARC), Giza 12618, Egypt
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Su Zar Chi Lwin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | | | - Mahmoud Zayda
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Monofiya 32897, Egypt
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Catherine Hofilena Damaso
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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Gong X, Zhang J, Gan Q, Teng Y, Hou J, Lyu Y, Liu Z, Wu Z, Dai R, Zou Y, Wang X, Zhu D, Zhu H, Liu T, Yan Y. Advancing microbial production through artificial intelligence-aided biology. Biotechnol Adv 2024; 74:108399. [PMID: 38925317 DOI: 10.1016/j.biotechadv.2024.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/20/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for value-added compound production. To optimize metabolism and reach optimal productivity, synthetic biology has developed various genetic devices to engineer microbial systems by gene editing, high-throughput protein engineering, and dynamic regulation. However, current synthetic biology methodologies still rely heavily on manual design, laborious testing, and exhaustive analysis. The emerging interdisciplinary field of artificial intelligence (AI) and biology has become pivotal in addressing the remaining challenges. AI-aided microbial production harnesses the power of processing, learning, and predicting vast amounts of biological data within seconds, providing outputs with high probability. With well-trained AI models, the conventional Design-Build-Test (DBT) cycle has been transformed into a multidimensional Design-Build-Test-Learn-Predict (DBTLP) workflow, leading to significantly improved operational efficiency and reduced labor consumption. Here, we comprehensively review the main components and recent advances in AI-aided microbial production, focusing on genome annotation, AI-aided protein engineering, artificial functional protein design, and AI-enabled pathway prediction. Finally, we discuss the challenges of integrating novel AI techniques into biology and propose the potential of large language models (LLMs) in advancing microbial production.
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Affiliation(s)
- Xinyu Gong
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jianli Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qi Gan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yuxi Teng
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jixin Hou
- School of ECAM, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Yanjun Lyu
- Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington 76019, USA
| | - Zhengliang Liu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Zihao Wu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Runpeng Dai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yusong Zou
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Xianqiao Wang
- School of ECAM, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Dajiang Zhu
- Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington 76019, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianming Liu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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Jian P, Liu J, Li L, Song Q, Zhang D, Zhang S, Chai C, Zhao H, Zhao G, Zhu H, Qiao J. AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44. J Dairy Sci 2024; 107:6576-6591. [PMID: 38762103 DOI: 10.3168/jds.2024-24754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 05/20/2024]
Abstract
Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) greater than that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multidrug resistance, and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR assays. Additionally, AcrR1 could repress the transcription of the nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.
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Affiliation(s)
- Pingqiu Jian
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Jiaheng Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China.
| | - Li Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Di Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Shenyi Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Chaofan Chai
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Hui Zhao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
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Chao M, Zhang Q, Huang L, Wang L, Dong J, Kou S, Song W, Wang T. ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance. Genes Genomics 2024:10.1007/s13258-024-01558-y. [PMID: 39214924 DOI: 10.1007/s13258-024-01558-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND ADP-glucose pyrophosphorylase (AGPase) is the key rate-limiting enzyme in starch biosynthesis pathway, and has been identified as a potential target for manipulation strategies aimed at improving crop yield and quality. OBJECTIVE To identify the AGPase gene family members in soybean, and explore the potential implications of GmAGPS2 in drought stress tolerance. METHODS The genome-wide identification and sequence analysis of soybean AGPase gene family was carried out by bioinformatics methods. The GmAGP gene expression was analyzed using transcriptome data and quantitative real-time PCR (qRT-PCR). Furthermore, transgenic yeast strains overexpressing GmAGPS2 were generated, and their growth was observed under drought stress. RESULTS In this study, we searched for AGPase genes (GmAGP) in the soybean genome and identified a total of 14 GmAGP genes. The GmAGP proteins had a unique conserved NTP_transferase domain and were mainly located in the chloroplast and cytosol. Evolutionarily, the GmAGP proteins can be clustered into two distinct subgroups; within the same subgroup, they displayed a similar distribution pattern of conserved motifs. The GmAGP genes exhibited an uneven distribution on 10 chromosomes, and segmental duplication contributed to AGPase gene family expansion in soybean. The GmAGP genes presented different tissue expression pattern, in which GmAGPL6, GmAGPL9, and GmAGPL10 mainly exhibited tissue-specific expression pattern. The promoter of GmAGP genes had multiple cis-acting elements related to phytohormones and stress responses, and 8 GmAGP genes contained drought-responsive cis-acting elements. qRT‒PCR analysis demonstrated a significant upregulation expression of GmAGPL6, GmAGPL10, and GmAGPS2 in response to drought stress. Further functional analysis indicated that GmAGPS2 gene could improve yeast growth under drought stress conditions and enhance the drought tolerance of yeast. CONCLUSION These results will contribute to further elucidation of the function of GmAGP genes, and offer important candidate genes for the genetic improvement of starch and yield-related traits and the breeding of high drought stress tolerance varieties in soybean.
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Affiliation(s)
- Maoni Chao
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Qiufang Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ling Huang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Li Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jie Dong
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Shibo Kou
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Weifeng Song
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Tiegu Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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Kuhlman BM, Diaz JH, Simon T, Reeves KD, Walker SJ, Atala A, Almeida-Porada G, Porada CD. Simulated microgravity impairs human NK cell cytotoxic activity against space radiation-relevant leukemic cells. NPJ Microgravity 2024; 10:85. [PMID: 39143086 PMCID: PMC11324864 DOI: 10.1038/s41526-024-00424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/04/2024] [Indexed: 08/16/2024] Open
Abstract
Natural killer (NK) cells are an important first-line of defense against malignant cells. Because of the potential for increased cancer risk from astronaut exposure to space radiation, we determined whether microgravity present during spaceflight affects the body's defenses against leukemogenesis. Human NK cells were cultured for 48 h under normal gravity and simulated microgravity (sμG), and cytotoxicity against K-562 (CML) and MOLT-4 (T-ALL) cells was measured using standard methodology or under continuous sμG. This brief exposure to sμG markedly reduced NK cytotoxicity against both leukemias, and these deleterious effects were more pronounced in continuous sμG. RNA-seq performed on NK cells from two additional healthy donors provided insight into the mechanism(s) by which sμG reduced cytotoxicity. Given our prior report of space radiation-induced human T-ALL in vivo, the reduced cytotoxicity against MOLT-4 is striking and raises the possibility that μG may increase astronaut risk of leukemogenesis during prolonged missions beyond LEO.
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Affiliation(s)
| | - Jonathan H Diaz
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
| | - Trang Simon
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
| | - Kimberly D Reeves
- Wake Forest Center for Precision Medicine, Winston Salem, NC, USA
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston Salem, NC, USA
| | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
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Albertini MR, Zuleger CL, Ranheim EA, Shiyanbola O, Sondel PM, Morris ZS, Eickhoff J, Newton MA, Ong IM, Schwartz RW, Hayim R, Kurzman ID, Turek M, Vail DM. Administration of intratumoral GD2-directed interleukin-2 immunocytokine and local radiation therapy to activate immune rejection of spontaneous canine melanoma. Melanoma Res 2024; 34:307-318. [PMID: 38768442 DOI: 10.1097/cmr.0000000000000975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Canine malignant melanoma provides a clinically relevant, large animal parallel patient population to study the GD2-reactive hu14.18-IL-2 immunocytokine as it is similar to human melanoma and expresses GD2. The objectives of this study were to evaluate safety, radiation fractionation, and identify informative biomarkers of an in-situ tumor vaccine involving local radiation therapy plus intratumoral-immunocytokine in melanoma tumor-bearing dogs. Twelve dogs (six dogs/arm) with locally advanced or metastatic melanoma were randomized to receive a single 8 Gy fraction (arm A) or three 8 Gy fractions over 1 week (arm B) to the primary site and regional lymph nodes (when clinically involved) with the single or last fraction 5 days before intratumoral-immunocytokine at 12 mg/m 2 on 3 consecutive days. Serial tumor biopsies were obtained. All 12 dogs completed protocol treatment, and none experienced significant or unexpected adverse events. Evidence of antitumor activity includes one dog with a complete response at day 60, one dog with a partial response at day 60, and four dogs with mixed responses. Histology of serial biopsies shows a variably timed increase in intratumoral lymphocytic inflammation in some dogs. Canine NanoString analyses of serial biopsies identified changes in gene signatures of innate and adaptive cell types versus baseline. There were no significant differences in NanoString results between arm A and arm B. We conclude that intratumoral-immunocytokine in combination with local radiation therapy in canine melanoma is well tolerated and has antitumor activity with the potential to inform clinical development in melanoma patients.
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Affiliation(s)
- Mark R Albertini
- University of Wisconsin Carbone Cancer Center
- Departments of, Medicine
- Dermatology, University of Wisconsin School of Medicine and Public Health
- The Medical Service, William S. Middleton Memorial Veterans Hospital
| | - Cindy L Zuleger
- University of Wisconsin Carbone Cancer Center
- Departments of, Medicine
| | - Erik A Ranheim
- University of Wisconsin Carbone Cancer Center
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Oyewale Shiyanbola
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Paul M Sondel
- University of Wisconsin Carbone Cancer Center
- Departments of Pediatrics
- Human Oncology
| | | | - Jens Eickhoff
- University of Wisconsin Carbone Cancer Center
- Biostatistics & Medical Informatics
| | - Michael A Newton
- University of Wisconsin Carbone Cancer Center
- Biostatistics & Medical Informatics
| | - Irene M Ong
- University of Wisconsin Carbone Cancer Center
- Biostatistics & Medical Informatics
- Obstetrics & Gynecology, University of Wisconsin School of Medicine and Public Health
| | | | | | | | - Michelle Turek
- Surgical Sciences, University of Wisconsin School of Veterinary Medicine, Madison, Wisconsin, USA
| | - David M Vail
- University of Wisconsin Carbone Cancer Center
- Departments of Medical Sciences
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9
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Gong S, Gan H, Chu J, Wang Z, Sun J. A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China. DNA Res 2024; 31:dsae021. [PMID: 38946223 PMCID: PMC11306577 DOI: 10.1093/dnares/dsae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/02/2024] Open
Abstract
Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.
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Affiliation(s)
- Shuai Gong
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Honghao Gan
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jianmin Chu
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, PR China
| | - Zhaoshan Wang
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jia Sun
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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10
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Bałdysz S, Nawrot R, Barylski J. "Tear down that wall"-a critical evaluation of bioinformatic resources available for lysin researchers. Appl Environ Microbiol 2024; 90:e0236123. [PMID: 38842338 PMCID: PMC11267937 DOI: 10.1128/aem.02361-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Lytic enzymes, or lysins for short, break down peptidoglycan and interrupt the continuity of the cell wall, which, in turn, causes osmotic lysis of the bacterium. Their ability to destroy bacteria from within makes them promising antimicrobial agents that can be used as alternatives or supplements to antibiotics. In this paper, we briefly summarize basic terms and concepts used to describe lysin sequences and delineate major lysin groups. More importantly, we describe the domain repertoire found in lysins and critically review bioinformatic tools or databases which are used in studies of these enzymes (with particular emphasis on the repositories of Hidden Markov models). Finally, we present a novel comprehensive, meticulously curated set of lysin-related family and domain models, sort them into clusters that reflect major families, and demonstrate that the selected models can be used to efficiently search for new lysins.
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Affiliation(s)
- Sophia Bałdysz
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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11
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Bechtel TD, Hershelman J, Ghoshal M, McLandsborough L, Gibbons JG. Chemical mutagenesis of Listeria monocytogenes for increased tolerance to benzalkonium chloride shows independent genetic underpinnings and off-target antibiotic resistance. PLoS One 2024; 19:e0305663. [PMID: 39028728 PMCID: PMC11259264 DOI: 10.1371/journal.pone.0305663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/02/2024] [Indexed: 07/21/2024] Open
Abstract
Listeria monocytogenes, a potentially fatal foodborne pathogen commonly found in food processing facilities, creates a significant economic burden that totals more than $2 billion annually in the United States due to outbreaks. Quaternary ammonium compounds (QACs), including benzalkonium chloride (BAC), are among the most widely used sanitizers to inhibit the growth and spread of L. monocytogenes from food processing facilities. However, resistance to QACs has been increasing in L. monocytogenes and different genetic mechanisms conferring resistance have been discovered. Here, we used ethyl methanesulfonate (EMS) to chemically mutagenize the BAC-susceptible strain, L. monocytogenes FSL-N1-304. We isolated two mutants with increased tolerance to BAC compared to the parental strain. Next, we assessed the off-target effect of increased tolerance to BAC by measuring the minimum inhibitory concentrations (MICs) of a diverse set of antibiotics, revealing that mut-1 and mut-2 displayed significantly increased resistance to fluoroquinolone antibiotics compared to the parental strain. A hemolysis assay was then used to investigate a potential correlation between BAC tolerance and virulence. Interestingly, mut-1 and mut-2 both exhibited significantly higher hemolysis percentage than the parental strain. We then sequenced the genomes of the parental strain and both mutants to identify mutations that may be involved in the increased resistance to BAC. We identified 3 and 29 mutations in mut-1 and mut-2, respectively. mut-1 contained nonsynonymous mutations in dagK (a diacylglycerol kinase), lmo2768 (a permease-encoding gene), and lmo0186 (resuscitation promoting factor). mut-2 contained a nonsense mutation in the nucleotide excision repair enzyme UvrABC system protein B encoding gene, uvrB, which likely accounts for the higher number of mutations observed. Transcriptome analysis in the presence of BAC revealed that genes related to the phosphotransferase system and internalins were up-regulated in both mutants, suggesting their significance in the BAC stress response. These two mutants provide insights into alternative mechanisms for increased BAC tolerance and could further our understanding of how L. monocytogenes persists in the food processing environment.
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Affiliation(s)
- Tyler D. Bechtel
- Department of Food Science, University of Massachusetts, Amherst, MA, United States of America
| | - Julia Hershelman
- Department of Food Science, University of Massachusetts, Amherst, MA, United States of America
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States of America
| | - Mrinalini Ghoshal
- Department of Food Science, University of Massachusetts, Amherst, MA, United States of America
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States of America
| | - Lynne McLandsborough
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States of America
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States of America
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States of America
- Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States of America
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12
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Chatterjee BK, Alam M, Chakravorty A, Lacy SM, Rech J, Brooks CL, Arvan PD, Truttmann MC. Small molecule FICD inhibitors suppress endogenous and pathologic FICD-mediated protein AMPylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603377. [PMID: 39071275 PMCID: PMC11275912 DOI: 10.1101/2024.07.13.603377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The AMP transferase, FICD, is an emerging drug target finetuning stress signaling in the endoplasmic reticulum (ER). FICD is a bi-functional enzyme, catalyzing both AMP addition (AMPylation) and removal (deAMPylation) from the ER resident chaperone BiP/GRP78. Despite increasing evidence linking excessive BiP/GRP78 AMPylation to human diseases, small molecules to inhibit pathogenic FICD variants are lacking. Using an in-vitro high-throughput screen, we identify two small-molecule FICD inhibitors, C22 and C73. Both molecules significantly inhibit FICD-mediated BiP/GRP78 AMPylation in intact cells while only weakly inhibiting BiP/GRP78 deAMPylation. C22 and C73 also efficiently inhibit pathogenic FICD variants and improve proinsulin processing in β cells. Our study identifies and validates FICD inhibitors, highlighting a novel therapeutic avenue against pathologic protein AMPylation.
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13
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Agha Gholizadeh M, Behjati F, Ghasemi Firouzabadi S, Heidari E, Razmara E, Almadani N, Sharifi Zarchi A, Garshasbi M. Novel splicing variant and gonadal mosaicism in DYRK1A gene identified by whole-genome sequencing in multiplex autism spectrum disorder families. Neurogenetics 2024:10.1007/s10048-024-00768-6. [PMID: 38976082 DOI: 10.1007/s10048-024-00768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with considerable genetic heterogeneity. The disorder is clinically diagnosed based on DSM-5 criteria, featuring deficits in social communication and interaction, along with restricted and repetitive behaviours. Here, we performed whole-genome sequencing (WGS) on four individuals with ASD from two multiplex families (MPX), where more than one individual is affected, to identify potential single nucleotide variants (SNVs) and structural variants (SVs) in coding and non-coding regions. A rigorous bioinformatics pipeline was employed for variant detection, followed by segregation analysis. Our investigation revealed an unreported splicing variant in the DYRK1A gene (c.-77 + 2T > C; IVS1 + 2T > C; NM_001396.5), in heterozygote form in two affected children in one of the families (family B), which was absent in the healthy parents and siblings. This finding suggests the presence of gonadal mosaicism in one of the parents, representing the first documented instance of such inheritance for a variant in the DYRK1A gene associated with ASD. Furthermore, we identified a 50 bp deletion in intron 9 of the DLG2 gene in two affected patients from the same family, confirmed by PCR and Sanger sequencing. In Family A, we identified potential candidate variants associated with ASD shared by the two patients. These findings enhance our understanding of the genetic landscape of ASD, particularly in MPX families, and highlight the utility of WGS in uncovering novel genetic contributions to neurodevelopmental disorders.
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Affiliation(s)
- Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Farkhondeh Behjati
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Erfan Heidari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Ali Sharifi Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Jalah-Al Ahmad Hwy, Tehran, 14117-1316, Iran.
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14
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Dasgupta P, Vinil K, Kanaujia SP. Evolutionary trends indicate a coherent organization of sap operons. Res Microbiol 2024:104228. [PMID: 38972435 DOI: 10.1016/j.resmic.2024.104228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Human hosts possess a complex network of immune responses against microbial pathogens. The production of antimicrobial peptides (AMPs), which target the pathogen cell membranes and inhibit them from inhabiting the hosts, is one such mechanism. However, pathogens have evolved systems that encounter these host-produced AMPs. The Sap (sensitivity to antimicrobial peptides) transporter uptakes AMPs inside the microbial cell and proteolytically degrades them. The Sap transporters comprise five subunits encoded by genes in an operon. Despite its ubiquitous nature, its subunits are not found to be in tandem with many organisms. In this study, a total of 421 Sap transporters were analyzed for their operonic arrangement. Out of 421, a total of 352 operons were found to be in consensus arrangement, while the remaining 69 show a varying arrangement of genes. The analysis of the intergenic distance between the subunits of the sap operon suggests a signature pattern with sapAB (-4), sapBC (-14), sapCD (-1), and sapDF (-4 to 1). An evolutionary analysis of these operons favors the consensus arrangement of the Sap transporter systems, substantiating its prevalence in most of the Gram-negative pathogens. Overall, this study provides insight into bacterial evolution, favoring the maintenance of the genetic organization of essential pathogenicity factors.
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Affiliation(s)
- Pratik Dasgupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Kavya Vinil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
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15
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Korhonen PK, La Rosa G, Sumanam SB, Gomez Morales MA, Ludovisi A, Pozio E, Tonanzi D, Chang BCH, Young ND, Gasser RB. Enhanced Genomic and Transcriptomic Resources for Trichinella pseudospiralis and T. spiralis to Underpin the Discovery of Molecular Differences between Stages and Species. Int J Mol Sci 2024; 25:7366. [PMID: 39000473 PMCID: PMC11242134 DOI: 10.3390/ijms25137366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Nematodes of the genus Trichinella are important pathogens of humans and animals. This study aimed to enhance the genomic and transcriptomic resources for T. pseudospiralis (non-encapsulated phenotype) and T. spiralis (encapsulated phenotype) and to explore transcriptional profiles. First, we improved the assemblies of the genomes of T. pseudospiralis (code ISS13) and T. spiralis (code ISS534), achieving genome sizes of 56.6 Mb (320 scaffolds, and an N50 of 1.02 Mb) and 63.5 Mb (568 scaffolds, and an N50 value of 0.44 Mb), respectively. Then, for each species, we produced RNA sequence data for three key developmental stages (first-stage muscle larvae [L1s], adults, and newborn larvae [NBLs]; three replicates for each stage), analysed differential transcription between stages, and explored enriched pathways and processes between species. Stage-specific upregulation was linked to cellular processes, metabolism, and host-parasite interactions, and pathway enrichment analysis showed distinctive biological processes and cellular localisations between species. Indeed, the secreted molecules calmodulin, calreticulin, and calsyntenin-with possible roles in modulating host immune responses and facilitating parasite survival-were unique to T. pseudospiralis and not detected in T. spiralis. These insights into the molecular mechanisms of Trichinella-host interactions might offer possible avenues for developing new interventions against trichinellosis.
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Affiliation(s)
- Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Giuseppe La Rosa
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sunita B Sumanam
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Maria Angeles Gomez Morales
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alessandra Ludovisi
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Edoardo Pozio
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Daniele Tonanzi
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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16
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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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17
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Li N, Yang Z, Wang J, Lin H. Drug-target interaction prediction using knowledge graph embedding. iScience 2024; 27:109393. [PMID: 38952679 PMCID: PMC11215290 DOI: 10.1016/j.isci.2024.109393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/16/2024] [Accepted: 02/28/2024] [Indexed: 07/03/2024] Open
Abstract
The prediction of drug-target interactions (DTIs) is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. Computational approaches to predicting DTIs can provide important insights into drug mechanisms of action. However, current methods for predicting DTIs based on the structural information of the knowledge graph may suffer from the sparseness and incompleteness of the knowledge graph and neglect the latent type information of the knowledge graph. In this paper, we propose TTModel, a knowledge graph embedding model for DTI prediction. By exploiting biomedical text and type information, TTModel can learn latent text semantics and type information to improve the performance of representation learning. Comprehensive experiments on two public datasets demonstrate that our model outperforms the state-of-the-art methods significantly on the task of DTI prediction.
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Affiliation(s)
- Nan Li
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Zhihao Yang
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Jian Wang
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Hongfei Lin
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
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18
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Soumbara T, Bonnet C, Hamed CT, Veten F, Hemeyine M, Fall-Malick FZ, El Yezid MM, Diallo A, Mounah MM, Houmeida A. Genetic variation of TLR3 gene is associated with the outcome of hepatitis b infection in mauritanian patients: case control study. BMC Infect Dis 2024; 24:616. [PMID: 38907187 PMCID: PMC11191147 DOI: 10.1186/s12879-024-09503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Toll-Like receptors (TLRs) play an important role in the immune response during hepatitis B virus (HBV) infection. In this study, we evaluated the association between two SNP variants (TLR3 rs3775290 and TLR4 rs4986790) and susceptibility to chronic HBV infection in Mauritania. SUBJECTS AND METHODS A total of 188 subjects were recruited for this study: 102 chronically infected patients and 86 individuals with spontaneously resolved HBV infection who were considered controls. Targeted PCR products were sequenced using Sanger sequencing. RESULTS We found that TLR3 rs3775290 was significantly more frequent in patients with chronic HBV than in the control population (p = 0.03). However, no association was found between the TLR4 rs3775290 polymorphism and chronic infection. CONCLUSION Our results suggest that the TLR3 rs3775290 polymorphism may be a risk factor for susceptibility to chronic HBV infection in the Mauritanian population.
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Affiliation(s)
- Tetou Soumbara
- Research Unit on Biomarkers in the Mauritanian Population, Faculty of Sciences and Technology, University of Nouakchott, Nouakchott, Mauritania
- National Institute of Hepato- Virology (INHV), Nouakchott, Mauritania
| | - Crystel Bonnet
- Institute of Hearing, Pasteur Institute, INSERM, Paris, 75012, France
| | | | - Fatimetou Veten
- National Institute of Hepato- Virology (INHV), Nouakchott, Mauritania
| | - Mohamed Hemeyine
- National Institute of Hepato- Virology (INHV), Nouakchott, Mauritania
| | | | | | - Aichetou Diallo
- National Institute of Hepato- Virology (INHV), Nouakchott, Mauritania
| | | | - Ahmed Houmeida
- Research Unit on Biomarkers in the Mauritanian Population, Faculty of Sciences and Technology, University of Nouakchott, Nouakchott, Mauritania.
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19
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Jackson TK, Rhode C. Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38885946 DOI: 10.1111/jfb.15844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/17/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.
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Affiliation(s)
- Tassin Kim Jackson
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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20
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Krause GR, Shands W, Wheeler TJ. Sensitive and error-tolerant annotation of protein-coding DNA with BATH. BIOINFORMATICS ADVANCES 2024; 4:vbae088. [PMID: 38966592 PMCID: PMC11223822 DOI: 10.1093/bioadv/vbae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
Summary We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes. Availability and implementation The software is available at https://github.com/TravisWheelerLab/BATH.
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Affiliation(s)
- Genevieve R Krause
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, United States
- Department of Computer Science, University of Montana, Missoula, MT 59812, United States
| | - Walt Shands
- Department of Computer Science, University of Montana, Missoula, MT 59812, United States
- Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, United States
| | - Travis J Wheeler
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, United States
- Department of Computer Science, University of Montana, Missoula, MT 59812, United States
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21
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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22
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Han H, Li X, Li T, Chen Q, Zhao J, Zhai H, Deng L, Meng X, Li C. Chromosome-level genome assembly of Solanum pimpinellifolium. Sci Data 2024; 11:577. [PMID: 38834611 DOI: 10.1038/s41597-024-03442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
Solanum pimpinellifolium, the closest wild relative of the domesticated tomato, has high potential for use in breeding programs aimed at developing multi-pathogen resistance and quality improvement. We generated a chromosome-level genome assembly of S. pimpinellifolium LA1589, with a size of 833 Mb and a contig N50 of 31 Mb. We anchored 98.80% of the contigs into 12 pseudo-chromosomes, and identified 74.47% of the sequences as repetitive sequences. The genome evaluation revealed BUSCO and LAI score of 98.3% and 14.49, respectively, indicating high quality of this assembly. A total of 41,449 protein-coding genes were predicted in the genome, of which 89.17% were functionally annotated. This high-quality genome assembly serves as a valuable resource for accelerating the biological discovery and molecular breeding of this important horticultural crop.
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Affiliation(s)
- Hongyu Han
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuhong Li
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Tianze Li
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Qian Chen
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiuhai Zhao
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Huawei Zhai
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Lei Deng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xianwen Meng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Chuanyou Li
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
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23
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Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y, Fei Z, Zheng Y. HortGenome Search Engine, a universal genomic search engine for horticultural crops. HORTICULTURE RESEARCH 2024; 11:uhae100. [PMID: 38863996 PMCID: PMC11165154 DOI: 10.1093/hr/uhae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Abstract
Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.
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Affiliation(s)
- Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shangxiao Wei
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yuling Deng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shaoyuan Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hua Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yijian Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hui Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yiding Wang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Renlong Zhang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Lu Ning
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
- Library, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
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24
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Meier-Schiesser B, Zecha C, Zierold S, Kolm I, Röckel M, Fröhlich W, Mittag N, Schmitt C, Kumbrink J, Hassel JC, Berking C, Nashan D, French LE, Vera-González J, Dummer R, Kerl-French K, Heinzerling L. Checkpoint inhibitor-induced lichen planus differs from spontaneous lichen planus on the clinical, histological, and gene expression level. JAAD Int 2024; 15:157-164. [PMID: 38882039 PMCID: PMC11180371 DOI: 10.1016/j.jdin.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 06/18/2024] Open
Abstract
Background Although highly efficacious, immune checkpoint inhibitors induce a multitude of immune-related adverse events including lichenoid skin reactions (irLP) that are often therapy-resistant. Objectives To compare the clinical, histological, and transcriptional features of irLP with spontaneous lichen planus (LP). Methods Clinical and histological presentations of irLP and LP, as well as the gene expression profiles of irLP and LP lesional and healthy skin were assessed. Results irLP differed considerably from LP with regard to the distribution pattern of skin lesions with irLP appearing mostly in an exanthematous form, whereas lesions were more localized in the LP group. Histologically, dermal lymphocyte infiltration was significantly lower in irLP compared with LP, whereas lymphocyte exocytosis and apoptotic keratinocytes were significantly higher in irLP. Gene expression analysis revealed irLP to have a more inflammatory profile with elevated IFNG levels and a possible role of phagosome signaling compared with LP. Limitations The study is descriptive and necessitates further investigation with larger cohorts and broader analyses. Conclusion irLP differs from spontaneous LP on the clinical, histopathological, and gene expression level. The inflammatory gene signature in irLP suggests that topical JAK inhibitors could be an effective treatment, targeting local skin inflammation without systemic immunosuppression.
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Affiliation(s)
| | - Christine Zecha
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Sarah Zierold
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Isabel Kolm
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Magdalena Röckel
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Waltraud Fröhlich
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Nora Mittag
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Christina Schmitt
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Joerg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Jessica C Hassel
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carola Berking
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Dorothee Nashan
- Department of Dermatology, Hospital Dortmund, Dortmund, Germany
| | - Lars Einar French
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | - Julio Vera-González
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Katrin Kerl-French
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Lucie Heinzerling
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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25
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Liu Y, Zhang Y, Chen Z, Peng J. POLAT: Protein function prediction based on soft mask graph network and residue-Label ATtention. Comput Biol Chem 2024; 110:108064. [PMID: 38677014 DOI: 10.1016/j.compbiolchem.2024.108064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/29/2024]
Abstract
MOTIVATION Elucidating protein function is a central problem in biochemistry, genetics, and molecular biology. Developing computational methods for protein function prediction is critical due to the significant gap between sequence and functional data. Recent advances in protein structure prediction, which strongly correlates with function, make it feasible to use structure to predict function. However, current structure-based methods overlook the fact that individual residues may contribute differently to the protein's function and do not take into account the correlation between protein residues and their functions. The challenge of effectively utilizing the relationship between protein residues and function-level information to predict protein function remains unsolved. RESULT We proposed a protein function prediction method based on Soft Mask Graph Networks and Residue-Label Attention (POLAT), which could combine sequence features, predicted structure features, and function-level information to get an accurate prediction. We use soft mask graph networks to adaptively extract the residues relevant to functions. A residue-label attention mechanism is adopted to obtain the protein-level encoded features of a protein, which are then concatenated with a protein-level embedding and fed into a dense classifier to determine the probabilities of each function. POLAT achieves 0.670, 0.515, 0.578 Fmax and 0.677, 0.409, 0.507 AUPR on the PDB cdhit test set for the MFO, BPO, and CCO domains, respectively, outperforming the existing structure-based SOTA method GAT-GO (Fmax 0.633, 0.492, 0.547; AUPR 0.660, 0.381, 0.479). POLAT is also competitive in extensive experiments among sequence-based and multimodal methods and achieves the SOTA performance in three out of six metrics.
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Affiliation(s)
- Yang Liu
- Intelligent Bioinformatics Laboratory, School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, 430070, China.
| | - Yi Zhang
- Intelligent Bioinformatics Laboratory, School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, 430070, China.
| | - ZiHao Chen
- Intelligent Bioinformatics Laboratory, School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, 430070, China.
| | - Jing Peng
- Intelligent Bioinformatics Laboratory, School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, 430070, China.
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26
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Nixon C, Lim SA, Sternke M, Barrick D, Harms MJ, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. Protein Sci 2024; 33:e5011. [PMID: 38747388 PMCID: PMC11094778 DOI: 10.1002/pro.5011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
A protein sequence encodes its energy landscape-all the accessible conformations, energetics, and dynamics. The evolutionary relationship between sequence and landscape can be probed phylogenetically by compiling a multiple sequence alignment of homologous sequences and generating common ancestors via Ancestral Sequence Reconstruction or a consensus protein containing the most common amino acid at each position. Both ancestral and consensus proteins are often more stable than their extant homologs-questioning the differences between them and suggesting that both approaches serve as general methods to engineer thermostability. We used the Ribonuclease H family to compare these approaches and evaluate how the evolutionary relationship of the input sequences affects the properties of the resulting consensus protein. While the consensus protein derived from our full Ribonuclease H sequence alignment is structured and active, it neither shows properties of a well-folded protein nor has enhanced stability. In contrast, the consensus protein derived from a phylogenetically-restricted set of sequences is significantly more stable and cooperatively folded, suggesting that cooperativity may be encoded by different mechanisms in separate clades and lost when too many diverse clades are combined to generate a consensus protein. To explore this, we compared pairwise covariance scores using a Potts formalism as well as higher-order sequence correlations using singular value decomposition (SVD). We find the SVD coordinates of a stable consensus sequence are close to coordinates of the analogous ancestor sequence and its descendants, whereas the unstable consensus sequences are outliers in SVD space.
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Affiliation(s)
- Charlotte Nixon
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Shion A. Lim
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Matt Sternke
- The T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- The T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Michael J. Harms
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Susan Marqusee
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- Department of ChemistryUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- California Institute for Quantitative Biosciences (QB3)BerkeleyCaliforniaUSA
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27
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Yuan JN, Ye ZX, Chen MN, Ren PP, Ning C, Sun ZT, Chen JP, Zhang CX, Li JM, Mao Q. Identification and Characterization of Three Novel Solemo-like Viruses in the White-Backed Planthopper, Sogatella furcifera. INSECTS 2024; 15:394. [PMID: 38921109 PMCID: PMC11203538 DOI: 10.3390/insects15060394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Agricultural insects play a crucial role in transmitting plant viruses and host a considerable number of insect-specific viruses (ISVs). Among these insects, the white-backed planthoppers (WBPH; Sogatella furcifera, Hemiptera: Delphacidae) are noteworthy rice pests and are responsible for disseminating the southern rice black-streaked dwarf virus (SRBSDV), a significant rice virus. In this study, we analyzed WBPH transcriptome data from public sources and identified three novel viruses. These newly discovered viruses belong to the plant-associated viral family Solemoviridae and were tentatively named Sogatella furcifera solemo-like virus 1-3 (SFSolV1-3). Among them, SFSolV1 exhibited a prevalent existence in different laboratory populations, and its complete genome sequence was obtained using rapid amplification of cDNA ends (RACE) approaches. To investigate the antiviral RNA interference (RNAi) response in WBPH, we conducted an analysis of virus-derived small interfering RNAs (vsiRNAs). The vsiRNAs of SFSolV1 and -2 exhibited typical patterns associated with the host's siRNA-mediated antiviral immunity, with a preference for 21- and 22-nt vsiRNAs derived equally from both the sense and antisense genomic strands. Furthermore, we examined SFSolV1 infection and distribution in WBPH, revealing a significantly higher viral load of SFSolV1 in nymphs' hemolymph compared to other tissues. Additionally, in adult insects, SFSolV1 exhibited higher abundance in male adults than in female adults.
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Affiliation(s)
- Jing-Na Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Meng-Nan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Peng-Peng Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Chao Ning
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Zong-Tao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
| | - Qianzhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.-N.Y.); (Z.-X.Y.); (M.-N.C.); (P.-P.R.); (C.N.); (Z.-T.S.); (J.-P.C.); (C.-X.Z.); (J.-M.L.)
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Ebott J, McAdams J, Kim C, Jansen C, Woodman M, De La Cruz P, Schrol C, Ribeiro J, James N. Enhanced amphiregulin exposure promotes modulation of the high grade serous ovarian cancer tumor immune microenvironment. Front Pharmacol 2024; 15:1375421. [PMID: 38831884 PMCID: PMC11144882 DOI: 10.3389/fphar.2024.1375421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
High grade serous ovarian cancer (HGSOC) is a lethal gynecologic malignancy in which chemoresistant recurrence rates remain high. Furthermore, HGSOC patients have demonstrated overall low response rates to clinically available immunotherapies. Amphiregulin (AREG), a low affinity epidermal growth factor receptor ligand is known to be significantly upregulated in HGSOC patient tumors following neoadjuvant chemotherapy exposure. While much is known about AREG's role in oncogenesis and classical immunity, it is function in tumor immunology has been comparatively understudied. Therefore, the objective of this present study was to elucidate how increased AREG exposure impacts the ovarian tumor immune microenvironment (OTIME). Using NanoString IO 360 and protein analysis, it was revealed that treatment with recombinant AREG led to prominent upregulation of genes associated with ovarian pathogenesis and immune evasion (CXCL8, CXCL1, CXCL2) along with increased STAT3 activation in HGSOC cells. In vitro co-culture assays consisting of HGSOC cells and peripheral blood mononuclear cells (PBMCs) stimulated with recombinant AREG (rAREG) led to significantly enhanced tumor cell viability. Moreover, PBMCs stimulated with rAREG exhibited significantly lower levels of IFNy and IL-2. In vivo rAREG treatment promoted significant reductions in circulating levels of IL-2 and IL-5. Intratumoral analysis of rAREG treated mice revealed a significant reduction in CD8+ T cells coupled with an upregulation of PD-L1. Finally, combinatorial treatment with an AREG neutralizing antibody and carboplatin led to a synergistic reduction of cell viability in HGSOC cell lines OVCAR8 and PEA2. Overall, this study demonstrates AREG's ability to modulate cytotoxic responses within the OTIME and highlights its role as a novel HGSOC immune target.
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Affiliation(s)
- Jasmine Ebott
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
- Department of Obstetrics and Gynecology, Warren-Alpert Medical School of Brown University, Providence, RI, United States
| | - Julia McAdams
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
| | - Chloe Kim
- School of Public Health, Brown University, Providence, RI, United States
| | - Corrine Jansen
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
- Department of Obstetrics and Gynecology, Warren-Alpert Medical School of Brown University, Providence, RI, United States
| | - Morgan Woodman
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Payton De La Cruz
- Pathobiology Graduate Program, Brown University, Providence, RI, United States
| | - Christoph Schrol
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Jennifer Ribeiro
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
- Department of Obstetrics and Gynecology, Warren-Alpert Medical School of Brown University, Providence, RI, United States
| | - Nicole James
- Women and Infants Hospital, Department of Obstetrics and Gynecology, Program in Women’s Oncology, Providence, RI, United States
- Department of Obstetrics and Gynecology, Warren-Alpert Medical School of Brown University, Providence, RI, United States
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Chen R, Yan J, Wickham JD, Gao Y. Genomic identification and evolutionary analysis of chemosensory receptor gene families in two Phthorimaea pest species: insights into chemical ecology and host adaptation. BMC Genomics 2024; 25:493. [PMID: 38762533 PMCID: PMC11102633 DOI: 10.1186/s12864-024-10428-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/17/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Insects rely on sophisticated sensitive chemosensory systems to sense their complex chemical environment. This sensory process involves a combination of odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) in the chemosensory system. This study focused on the identification and characterization of these three types of chemosensory receptor genes in two closely related Phthorimaea pest species, Phthorimaea operculella (potato tuber moth) and Phthorimaea absoluta (tomato leaf miner). RESULTS Based on manual annotation of the genome, we identified a total of 349 chemoreceptor genes from the genome of P. operculella, including 93 OR, 206 GR and 50 IR genes, while for P. absoluta, we identified 72 OR, 122 GR and 46 IR genes. Through phylogenetic analysis, we observed minimal differences in the number and types of ORs and IRs between the potato tuber moth and tomato leaf miner. In addition, we found that compared with those of tomato leaf miners, the gustatory receptor branch of P. operculella has undergone a large expansion, which may be related to P. absoluta having a narrower host range than P. operculella. Through analysis of differentially expressed genes (DEGs) of male and female antennae, we uncovered 45 DEGs (including 32ORs, 9 GRs, and 4 IRs). CONCLUSIONS Our research provides a foundation for exploring the chemical ecology of these two pests and offers new insights into the dietary differentiation of lepidopteran insects, while simultaneously providing molecular targets for developing environmentally friendly pest control methods based on insect chemoreception.
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Affiliation(s)
- Ruipeng Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junjie Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jacob D Wickham
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, 119071, Russia
- Department of Entomology, Rutgers University, 93 Lipman Drive, New Brunswick, New Jersey, USA
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Cai Y, Anderson E, Xue W, Wong S, Cui L, Cheng X, Wang O, Mao Q, Liu SJ, Davis JT, Magalang PR, Schmidt D, Kasuga T, Garbelotto M, Drmanac R, Kua CS, Cannon C, Maloof JN, Peters BA. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3 (BETHESDA, MD.) 2024; 14:jkae043. [PMID: 38427916 PMCID: PMC11075539 DOI: 10.1093/g3journal/jkae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome, enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.
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Affiliation(s)
- Ying Cai
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Ellis Anderson
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Wen Xue
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sylvia Wong
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Luman Cui
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofang Cheng
- Department of Research, MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ou Wang
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Mao
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sophie Jia Liu
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - John T Davis
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Paulo R Magalang
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Douglas Schmidt
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service, Davis, CA 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Chai-Shian Kua
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Charles Cannon
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
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Armah-Sekum RE, Szedmak S, Rousu J. Protein function prediction through multi-view multi-label latent tensor reconstruction. BMC Bioinformatics 2024; 25:174. [PMID: 38698340 PMCID: PMC11067221 DOI: 10.1186/s12859-024-05789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND In last two decades, the use of high-throughput sequencing technologies has accelerated the pace of discovery of proteins. However, due to the time and resource limitations of rigorous experimental functional characterization, the functions of a vast majority of them remain unknown. As a result, computational methods offering accurate, fast and large-scale assignment of functions to new and previously unannotated proteins are sought after. Leveraging the underlying associations between the multiplicity of features that describe proteins could reveal functional insights into the diverse roles of proteins and improve performance on the automatic function prediction task. RESULTS We present GO-LTR, a multi-view multi-label prediction model that relies on a high-order tensor approximation of model weights combined with non-linear activation functions. The model is capable of learning high-order relationships between multiple input views representing the proteins and predicting high-dimensional multi-label output consisting of protein functional categories. We demonstrate the competitiveness of our method on various performance measures. Experiments show that GO-LTR learns polynomial combinations between different protein features, resulting in improved performance. Additional investigations establish GO-LTR's practical potential in assigning functions to proteins under diverse challenging scenarios: very low sequence similarity to previously observed sequences, rarely observed and highly specific terms in the gene ontology. IMPLEMENTATION The code and data used for training GO-LTR is available at https://github.com/aalto-ics-kepaco/GO-LTR-prediction .
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Affiliation(s)
- Robert Ebo Armah-Sekum
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland.
| | - Sandor Szedmak
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland
| | - Juho Rousu
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland.
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Miguel-Ruano V, Feltzer R, Batuecas MT, Ramachandran B, El-Araby AM, Avila-Cobian LF, De Benedetti S, Mobashery S, Hermoso JA. Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A. Int J Biol Macromol 2024; 267:131420. [PMID: 38583835 PMCID: PMC11327851 DOI: 10.1016/j.ijbiomac.2024.131420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Natural product bulgecin A potentiates the activity of β-lactam antibiotics by inhibition of three lytic transglycosylases in Pseudomonas aeruginosa, of which MltD is one. MltD exhibits both endolytic and exolytic reactions in the turnover of the cell-wall peptidoglycan and tolerates the presence or absence of stem peptides in its substrates. The present study reveals structural features of the multimodular MltD, presenting a catalytic module and four cell-wall-binding LysM modules that account for these attributes. Three X-ray structures are reported herein for MltD that disclose one unpredicted LysM module tightly attached to the catalytic domain, whereas the other LysM modules are mobile, and connected to the catalytic domain through long flexible linkers. The formation of crystals depended on the presence of bulgecin A. The expansive active-site cleft is highlighted by the insertion of a helical region, a hallmark of the family 1D of lytic transglycosylases, which was mapped out in a ternary complex of MltD:bulgecinA:chitotetraose, revealing at the minimum the presence of eight subsites (from -4 to +4, with the seat of reaction at subsites -1 and + 1) for binding of sugars of the substrate for the endolytic reaction. The mechanism of the exolytic reaction is revealed in one of the structures, showing how the substrate's terminal anhydro-NAM moiety could be sequestered at subsite +2. Our results provide the structural insight for both the endolytic and exolytic activities of MltD during cell-wall-turnover events.
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Balajee Ramachandran
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Amr M El-Araby
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Luis F Avila-Cobian
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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Abu-Romman A, Scholand KK, Govindarajan G, Yu Z, Pal-Ghosh S, Stepp MA, de Paiva CS. Age-Related Differences in the Mouse Corneal Epithelial Transcriptome and Their Impact on Corneal Wound Healing. Invest Ophthalmol Vis Sci 2024; 65:21. [PMID: 38739085 PMCID: PMC11098051 DOI: 10.1167/iovs.65.5.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
Purpose Aging is a risk factor for dry eye. We sought to identify changes in the aged mouse corneal epithelial transcriptome and determine how age affects corneal sensitivity, re-epithelialization, and barrier reformation after corneal debridement. Methods Corneal epithelium of female C57BL/6J (B6) mice of different ages (2, 12, 18, and 24 months) was collected, RNA extracted, and bulk RNA sequencing performed. Cornea sensitivity was measured with an esthesiometer in 2- to 3-month-old, 12- to 13-month-old, 18- to 19-month-old, and 22- to 25-month-old female and male mice. The 2-month-old and 18-month-old female and male mice underwent unilateral corneal debridement using a blunt blade. Wound size and fluorescein staining were visualized and photographed at different time points, and a re-epithelialization rate curve was calculated. Results There were 157 differentially expressed genes in aged mice compared with young mice. Several pathways downregulated with age control cell migration, proteoglycan synthesis, and collagen trimerization, assembly, biosynthesis, and degradation. Male mice had decreased corneal sensitivity compared with female mice at 12 and 24 months of age. Aged mice, irrespective of sex, had delayed corneal re-epithelialization in the first 48 hours and worse corneal fluorescein staining intensity at day 14 than young mice. Conclusions Aged corneal epithelium has an altered transcriptome. Aged mice regardless of sex heal more slowly and displayed more signs of corneal epithelial defects after wounding than young mice. These results indicate that aging significantly alters the corneal epithelium and its ability to coordinate healing.
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Affiliation(s)
- Anmar Abu-Romman
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Kaitlin K. Scholand
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
- Department of Biosciences, Rice University, Houston, Texas, United States
| | - Gowthaman Govindarajan
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Zhiyuan Yu
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Sonali Pal-Ghosh
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Mary A. Stepp
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Department of Ophthalmology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Cintia S. de Paiva
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
- Department of Biosciences, Rice University, Houston, Texas, United States
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Zheng R, Feng Y, Kong L, Wu X, Zhou J, Zhang L, Liu S. Blue-light irradiation induced partial nitrification. WATER RESEARCH 2024; 254:121381. [PMID: 38442606 DOI: 10.1016/j.watres.2024.121381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/08/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.
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Affiliation(s)
- Ru Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Lingrui Kong
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Liguo Zhang
- School of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China.
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Porada C, Kuhlman B, Diaz J, Simon T, Reaves K, Walker S, Atala A, Almeida-Porada G. Simulated Microgravity Impairs Human NK Cell Cytotoxic Activity Against Space Radiation-Relevant Leukemic Cells. RESEARCH SQUARE 2024:rs.3.rs-3972868. [PMID: 38746365 PMCID: PMC11092860 DOI: 10.21203/rs.3.rs-3972868/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Natural killer (NK) cells are important effectors of the innate immune system. Unlike T cells, NK cells do not require antigen-priming, making them an important first-line of defense against malignant cells. Because of the potential for increased cancer risk as a result of astronaut exposure to space radiation, we performed studies to determine whether conditions of microgravity present during spaceflight affects the body's natural defenses against leukemogenesis. Human NK cells were cultured for 48 hours under normal gravity and simulated microgravity (sµG), and cytotoxicity against K-562 (CML) and MOLT-4 (T-ALL) cell lines was measured using standard methodology or under continuous conditions of sµG. Even this brief exposure to sµG markedly reduced NK cytotoxicity against both leukemic cells using standard assay procedures, and these deleterious effects were even more pronounced in continuous sµG. RNA-seq performed on NK cells from two healthy donors provided insight into the mechanism(s) by which sµG reduced cytotoxicity. Given our prior report that human HSC exposed to simulated space radiation gave rise to T-ALL in vivo , the reduced cytotoxicity against MOLT-4 is striking and raises the possibility that µG may add to astronaut risk of leukemogenesis during prolonged missions beyond LEO.
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Pires GP, Fioresi VS, Canal D, Canal DC, Fernandes M, Brustolini OJB, de Avelar Carpinetti P, Ferreira A, da Silva Ferreira MF. Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers. Sci Rep 2024; 14:9811. [PMID: 38684872 PMCID: PMC11059378 DOI: 10.1038/s41598-024-60417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.
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Affiliation(s)
- Giovanna Pinto Pires
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Vinicius Sartori Fioresi
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Drielli Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Dener Cezati Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Miquéias Fernandes
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Otávio José Bernardes Brustolini
- Laboratório Nacional de Computação Científica (LNCC). Av. Getulio Vargas, 333, Petrópolis, Rio de Janeiro, Quitandinha, 25651-076, Brazil
| | - Paola de Avelar Carpinetti
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil.
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Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024; 15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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Affiliation(s)
- Lucas Serra Moncadas
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.
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van den Herik B, Bergonzi S, Li Y, Bachem CW, ten Tusscher KH. A coordinated switch in sucrose and callose metabolism enables enhanced symplastic unloading in potato tubers. QUANTITATIVE PLANT BIOLOGY 2024; 5:e4. [PMID: 38689753 PMCID: PMC11058582 DOI: 10.1017/qpb.2024.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 05/02/2024]
Abstract
One of the early changes upon tuber induction is the switch from apoplastic to symplastic unloading. Whether and how this change in unloading mode contributes to sink strength has remained unclear. In addition, developing tubers also change from energy to storage-based sucrose metabolism. Here, we investigated the coordination between changes in unloading mode and sucrose metabolism and their relative role in tuber sink strength by looking into callose and sucrose metabolism gene expression combined with a model of apoplastic and symplastic unloading. Gene expression analysis suggests that callose deposition in tubers is decreased by lower callose synthase expression. Furthermore, changes in callose and sucrose metabolism are strongly correlated, indicating a well-coordinated developmental switch. Modelling indicates that symplastic unloading is not the most efficient unloading mode per se. Instead, it is the concurrent metabolic switch that provides the physiological conditions necessary to potentiate symplastic transport and thereby enhance tuber sink strength .
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Affiliation(s)
- Bas van den Herik
- Computational Developmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Sara Bergonzi
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Yingji Li
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Christian W. Bachem
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
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Darvishi F, Beiranvand E, Kalhor H, Shahbazi B, Mafakher L. Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase. Int J Biol Macromol 2024; 263:130312. [PMID: 38403216 DOI: 10.1016/j.ijbiomac.2024.130312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/10/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
L-Asparaginase is a key component in the treatment of leukemias and lymphomas. However, the glutamine affinity of this therapeutic enzyme is an off-target activity that causes several side effects. The modeling and molecular docking study of Yarrowia lipolytica L-asparaginase (YL-ASNase) to reduce its l-glutamine affinity and increase its stability was the aim of this study. Protein-ligand interactions of wild-type and different mutants of YL-ASNase against L-asparagine compared to l-glutamine were assessed using AutoDock Vina tools because the crystal structure of YL-ASNase does not exist in the protein data banks. The results showed that three mutants, T171S, T171S-N60A, and T171A-T223A, caused a considerable increase in L-asparagine affinity and a decrease in l-glutamine affinity as compared to the wild-type and other mutants. Then, molecular dynamics simulation and MM/GBSA free energy were applied to assess the stability of protein structure and its interaction with ligands. The three mutated proteins, especially T171S-N60A, had higher stability and interactions with L-asparagine than l-glutamine in comparison with the wild-type. The YL-ASNase mutants could be introduced as appropriate therapeutic candidates that might cause lower side effects. However, the functional properties of these mutated enzymes need to be confirmed by genetic manipulation and in vitro and in vivo studies.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran.
| | - Elham Beiranvand
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Dong Z, Wang J, Chen G, Guo Y, Zhao N, Wang Z, Zhang B. A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis. Sci Data 2024; 11:322. [PMID: 38548787 PMCID: PMC10978949 DOI: 10.1038/s41597-024-03173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.
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Affiliation(s)
- Zhongdian Dong
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiangman Wang
- Qingdao Marine Management Support Center, Qingdao, Shandong, China
| | - Guozhu Chen
- National Plateau Wetland Research Center, College of Wetlands, Southwest Forestry University, Kunming, 650224, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Na Zhao
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory-Zhanjiang, Zhanjiang, 524000, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Bo Zhang
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory-Zhanjiang, Zhanjiang, 524000, China.
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Li Z, Na Wu X, Jacquot A, Chaput V, Adamo M, Neuhäuser B, Straub T, Lejay L, Schulze WX. Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2127-2142. [PMID: 38066636 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 03/28/2024]
Abstract
NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.
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Affiliation(s)
- Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Aurore Jacquot
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Valentin Chaput
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Mattia Adamo
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Benjamin Neuhäuser
- Department of Crop Physiology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Tatsiana Straub
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Laurence Lejay
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
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Bucchieri D, Mangiagalli M, Martani F, Butti P, Lotti M, Serra I, Branduardi P. A novel laccase from Trametes polyzona with high performance in the decolorization of textile dyes. AMB Express 2024; 14:32. [PMID: 38506984 PMCID: PMC10954600 DOI: 10.1186/s13568-024-01687-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Laccases are multicopper oxidases able to oxidize several phenolic compounds and find application in numerous industrial applications. Among laccase producers, white-rot fungi represent a valuable source of multiple isoforms and isoenzymes of these multicopper oxidases. Here we describe the identification, biochemical characterization, and application of laccase 2 from Trametes polyzona (TP-Lac2), a basidiomycete fungus emerged among others that have been screened by plate assay. This enzyme has an optimal temperature of 50 °C and in acidic conditions it is able to oxidize both phenolic and non-phenolic compounds. The ability of TP-Lac2 to decolorize textile dyes was tested in the presence of natural and synthetic mediators at 30 °C and 50 °C. Our results indicate that TP-Lac2 most efficiently decolorizes (decolorization rate > 75%) malachite green oxalate, orange G, amido black10B and bromocresol purple in the presence of acetosyringone and 2,2'-azinobis (3-ethylbenzthiazoline-6-sulfonate)-ABTS. Overall, the laccase mediator system consisting of TP-Lac2 and the natural mediator acetosyringone has potential as an environmentally friendly alternative for wastewater treatment in the textile industry.
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Affiliation(s)
- Daniela Bucchieri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
- Department of Material Science and Nanotechnology, CORIMAV Program, University of Milano-Bicocca, Via R. Cozzi 55, 20125, Milano, Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
| | - Pietro Butti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
| | - Immacolata Serra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy.
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milano, Italy
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Saha S, Mandal SK, Kanaujia SP. Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries. J Biomol Struct Dyn 2024:1-18. [PMID: 38450736 DOI: 10.1080/07391102.2024.2325670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
5-Methylcytosine methyltransferases (m5C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a complete understanding of the archaeal counterparts is lacking. In this study, the identification and characterization of archaeal RNA m5C MTases were performed. As a case study, a hyperthermophilic archaeon, Pyrococcus horikoshii OT3, which possesses five putative RNA m5C MTases, was chosen. Among the five putative RNA m5C MTases, two proteins (PH0851 and PH1991) have been characterized as homologs of a bacterial rRNA MTase (RsmB) and eukaryal tRNA MTase (NSUN6), respectively. The in-depth characterization of the remaining three putative RNA m5C MTases (PH1078, PH1374, and PH1537) in this study suggests the presence of the signature architecture and catalytic residues plausibly involved in the binding of their cognate RNA substrates. Additionally, the results also suggest the existence of two RsmB-like proteins (PH0851 and PH1078) belonging to the same subfamily IV of m5C RNA MTase. However, the proteins PH1374 and PH1537 belong to the same subfamily V but bind to different substrates, rRNA and tRNA, respectively. The findings further indicate that archaeal RNA m5C MTases link those from bacteria and eukarya.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayan Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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Liu X, Li K, Yu J, Ma C, Che Q, Zhu T, Li D, Pfeifer BA, Zhang G. Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering. Metab Eng 2024; 82:147-156. [PMID: 38382797 DOI: 10.1016/j.ymben.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust cFF production system which entailed stepwise engineering of the filamentous fungal strain Aspergillus nidulans A1145 as a heterologous expression host. We first established a preliminary cFF producing strain by introducing the heterologous nonribosomal peptide synthetase (NRPS) gene penP1 to A. nidulans A1145. Key metabolic pathways involving shikimate and aromatic amino acid biosynthetic support were then engineered through a combination of gene deletions of competitive pathway steps, over-expressing feedback-insensitive enzymes in phenylalanine biosynthesis, and introducing a phosphoketolase-based pathway, which diverted glycolytic flux toward the formation of erythrose 4-phosphate (E4P). Through the stepwise engineering of A. nidulans A1145 outlined above, involving both heterologous pathway addition and native pathway metabolic engineering, we were able to produce cFF with titers reaching 611 mg/L in shake flask culture and 2.5 g/L in bench-scale fed-batch bioreactor culture. Our study establishes a production platform for cFF biosynthesis and successfully demonstrates engineering of phenylalanine derived diketopiperazines in a filamentous fungal host.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, United States.
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China; Lab of Marine Medicinal Resources Discovery, Marine Biomedical Research Institute of Qingdao, Qingdao, 266075, China.
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Tripathi D, Kapoor A, Bulbul, Pankaj, Kant R, Saluja D, Sharma M. Functional annotation of Candida albicans hypothetical proteins: a bioinformatics approach. Arch Microbiol 2024; 206:118. [PMID: 38393407 DOI: 10.1007/s00203-024-03840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 01/07/2024] [Indexed: 02/25/2024]
Abstract
Candida albicans is a member of the ascomycetes class of fungi and it is an opportunistic pathogen species responsible for a wide range of fungal infections in humans. Bioinformatics and sequencing analysis of Candida proteomics has disclosed that around 69% proteome is still uncharacterized which needs to be annotated with functions. The NCBI-Genome has termed them as hypothetical proteins (HPs) in the whole proteome of Candida. Interpretation of this substantial portion of the proteome can reveal novel pharmacological targets for markers, drug development, and other therapeutics and so on. In this article, we have assigned functional annotation to these hypothetical proteins using bioinformatics methodologies. The advanced and robust computational models have been used to assign the preliminary functions to these putative HPs with high level of confidence. The findings of this study unveil some novel pharmacological targets for drug therapy and vaccines and it would help to identify novel molecular mechanisms underlying the fungal pathogenesis.
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Affiliation(s)
- Deepika Tripathi
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Arushi Kapoor
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Bulbul
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Pankaj
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Ravi Kant
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Daman Saluja
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Meenakshi Sharma
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India.
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Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
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Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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48
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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Ayadi I, Nebli S, Ben Marzoug R, Rebai A. Charge cluster occurrence in land plants' mitochondrial proteomes with functional and structural insights. J Biomol Struct Dyn 2024:1-11. [PMID: 38345014 DOI: 10.1080/07391102.2024.2313154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/25/2024] [Indexed: 03/22/2024]
Abstract
The Charge Clusters (CCs) are involved in key functions and are distributed according to the organism, the protein's type, and the charge of amino acids. In the present study, we have explored the occurrence, position, and annotation as a first large-scale study of the CCs in land plants mitochondrial proteomes. A new python script was used for data curation. The Finding Clusters Charge in Protein Sequences Program was performed after adjusting the reading window size. A 44316 protein sequences belonging to 52 species of land plants were analysed. The occurrence of Negative Charge Clusters (NCCs) (1.2%) is two times more frequent than the Positive Charge Clusters (PCCs) (0.64%). Moreover, 39 and 30 NCCs were conserved in 88 and 41 proteins in intra and in inter proteomes respectively, while 14 and 21 PCCs were conserved in 53 and 85 protein sequences in intra and inter proteomes consecutively. Sequences carrying mixed CCs are rare (0.12%). Despite this low abundance, CCs play a crucial role in protein function. The CCs tend to be located mainly in the terminal regions of proteins which guarantees specific protein targeting and import into the mitochondria. In addition, the functional annotation of CCs according to Gene Ontology shows that CCs are involved in binding functions of either proteins or macromolecules which are deployed in different metabolic and cellular processes such as RNA editing and transcription. This study may provide valuable information while considering the CCs in understanding the environmental adaptation of plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Syrine Nebli
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Yu C, Wang P, Zhang S, Liu J, Cheng Y, Zhang S, Wu Z. Passionfruit Genomic Database (PGD): a comprehensive resource for passionfruit genomics. BMC Genomics 2024; 25:157. [PMID: 38331722 PMCID: PMC10851451 DOI: 10.1186/s12864-024-10069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Passionfruit (Passiflora edulis) is a significant fruit crop in the commercial sector, owing to its high nutritional and medicinal value. The advent of high-throughput genomics sequencing technology has led to the publication of a vast amount of passionfruit omics data, encompassing complete genome sequences and transcriptome data under diverse stress conditions. To facilitate the efficient integration, storage, and analysis of these large-scale datasets, and to enable researchers to effectively utilize these omics data, we developed the first passionfruit genome database (PGD). The PGD platform comprises a diverse range of functional modules, including a genome browser, search function, heatmap, gene expression patterns, various tools, sequence alignment, and batch download, thereby providing a user-friendly interface. Additionally, supplementary practical tools have been developed for the PGD, such as gene family analysis tools, gene ontology (GO) terms, a pathway enrichment analysis, and other data analysis and mining tools, which enhance the data's utilization value. By leveraging the database's robust scalability, the intention is to continue to collect and integrate passionfruit omics data in the PGD, providing comprehensive and in-depth support for passionfruit research. The PGD is freely accessible via http://passionfruit.com.cn .
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Affiliation(s)
- Chaowei Yu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China
| | - Peng Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China
| | - Shengjie Zhang
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jindian Liu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingyin Cheng
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China.
| | - Zujian Wu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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