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Tran Van Canh L, Aubourg S. Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides. Methods Mol Biol 2024; 2731:3-21. [PMID: 38019422 DOI: 10.1007/978-1-0716-3511-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Genes encoding small secreted peptides are widely distributed among plant genomes but their detection and annotation remains challenging. The bioinformatics protocol described here aims to identify as exhaustively as possible secreted peptide precursors belonging to a family of interest. First, homology searches are performed at the protein and genome levels. Next, multiple sequence alignments and predictions of a secretion signal are used to define a set of homologous proteins sharing features of secreted peptide precursors. These protein sequences are then used as input of motif detection and profile-based tools to build representative matrices and profiles that are used iteratively as guides to scan again the proteome and genome until family completion.
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Affiliation(s)
- Loup Tran Van Canh
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
| | - Sébastien Aubourg
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
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Cheng Y, Chen X, Liu W, Yang L, Wu J, Wang Y, Yu W, Zhou J, Fayyaz P, Luo ZB, Deng S, Shi W. Homolog of Human placenta-specific gene 8, PcPLAC8-10, enhances cadmium uptake by Populus roots. J Hazard Mater 2023; 460:132349. [PMID: 37657324 DOI: 10.1016/j.jhazmat.2023.132349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/03/2023]
Abstract
Cadmium (Cd) pollution of soil occurs worldwide. Phytoremediation is an effective approach for cleaning up Cd polluted soil. Fast growing Populus species with high Cd uptake capacities are desirable for phytoremediation. Thus, it is important to elucidate the molecular functions of genes involved in Cd uptake by poplars. In this study, PcPLAC8-10, a homolog of Human placenta-specific gene 8 (PLAC8) implicated in Cd transport was functionally characterized in Populus × canescens. PcPLAC8-10 was transcriptionally induced in Cd-treated roots and it encoded a plasma membrane-localized transporter. PcPLAC8-10 exhibited Cd uptake activity when expressed in yeast cells. No difference in growth was observed between wild type (WT) and PcPLAC8-10-overexpressing poplars. PcPLAC8-10-overexpressing poplars exhibited increases in net Cd2+ influxes by 192% and Cd accumulation by 57% in the roots. However, similar reductions in biomass were found in WT and transgenic poplars when exposed to Cd. The complete motif of CCXXXXCPC in PcPLAC8-10 was essential for its Cd transport activity. These results suggest that PcPLAC8-10 is a plasma membrane-localized transporter responsible for Cd uptake in the roots and the complete CCXXXXCPC motif of PcPLAC8-10 plays a key role in its Cd transport activity in poplars.
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Affiliation(s)
- Yao Cheng
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xin Chen
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Wenzhe Liu
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lingyu Yang
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jiangting Wu
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Yang Wang
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Wenjian Yu
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jing Zhou
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Payam Fayyaz
- Forest, Range and Watershed Management Department, Agriculture and Natural Resources Faculty, Yasouj University, Yasuj 75919 63179, Islamic Republic of Iran
| | - Zhi-Bin Luo
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China; Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, PR China; Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying, Shandong Province 257000, PR China.
| | - Shurong Deng
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Wenguang Shi
- National Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
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Aydemir MN, Aydemir HB, Budak M, Kızıltepe B, Çelebi MŞ, Korkmaz EM, Başıbüyük HH. A novel, conserved and possibly functional motif "WHWGHTW" in mitochondrial transcription across Bilateria. Mitochondrion 2023; 68:72-80. [PMID: 36400160 DOI: 10.1016/j.mito.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/22/2022] [Accepted: 11/05/2022] [Indexed: 11/17/2022]
Abstract
The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of 'WWWGHTW' were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.
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Affiliation(s)
- Merve Nur Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey.
| | - Habeş Bilal Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey
| | - Mahir Budak
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Birsel Kızıltepe
- Sivas Cumhuriyet University, Graduate School of Natural and Applied Sciences, Department of Bioinformatics, 58140 Sivas, Turkey
| | - Melissa Şafak Çelebi
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Ertan Mahir Korkmaz
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Hasan Hüseyin Başıbüyük
- Akdeniz University, Faculty of Health Sciences, Department of Gerontology, 07070 Antalya, Turkey
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Chen K, Zhang M, Xu L, Yi Y, Wang L, Wang H, Wang Z, Xing J, Li P, Zhang X, Shi X, Ye M, Osbourn A, Qiao X. Identification of oxidosqualene cyclases associated with saponin biosynthesis from Astragalus membranaceus reveals a conserved motif important for catalytic function. J Adv Res 2022; 43:247-257. [PMID: 36585112 PMCID: PMC9811366 DOI: 10.1016/j.jare.2022.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/10/2022] [Accepted: 03/22/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Triterpenoids and saponins have a broad range of pharmacological activities. Unlike most legumes which contain mainly oleanane-type scaffold, Astragalus membranaceus contains not only oleanane-type but also cycloartane-type saponins, for which the biosynthetic pathways are unknown. OBJECTIVES This work aims to study the function and catalytic mechanism of oxidosqualene cyclases (OSCs), one of the most important enzymes in triterpenoid biosynthesis, in A. membranaceus. METHODS Two OSC genes, AmOSC2 and AmOSC3, were cloned from A. membranaceus. Their functions were studied by heterologous expression in tobacco and yeast, together with in vivo transient expression and virus-induced gene silencing. Site-directed mutagenesis and molecular docking were used to explain the catalytic mechanism for the conserved motif. RESULTS AmOSC2 is a β-amyrin synthase which showed higher expression levels in underground parts. It is associated with the production of β-amyrin and soyasaponins (oleanane-type) in vivo. AmOSC3 is a cycloartenol synthase expressed in both aerial and underground parts. It is related to the synthesis of astragalosides (cycloartane-type) in the roots, and to the synthesis of cycloartenol as a plant sterol precursor. From AmOSC2/3, conserved triad motifs VFM/VFN were discovered for β-amyrin/cycloartenol synthases, respectively. The motif is a critical determinant of yield as proved by 10 variants from different OSCs, where the variant containing the conserved motif increased the yield by up to 12.8-fold. Molecular docking and mutagenesis revealed that Val, Phe and Met residues acted together to stabilize the substrate, and the cation-π interactions from Phe played the major role. CONCLUSION The study provides insights into the biogenic origin of oleanane-type and cycloartane-type triterpenoids in Astragalus membranaceus. The conserved motif offers new opportunities for OSC engineering.
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Affiliation(s)
- Kuan Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Lulu Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Linlin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Haotian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Zilong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jiangtao Xing
- Thermo Fisher Scientific, Building A, Qiming Plaza, No.101, Wangjing Lize Middle Street, Beijing 100102, China
| | - Pi Li
- Thermo Fisher Scientific, Building A, Qiming Plaza, No.101, Wangjing Lize Middle Street, Beijing 100102, China
| | - Xiaohui Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom,Corresponding authors at: State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China (X. Qiao); Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A. Osbourn).
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China,Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom,Corresponding authors at: State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China (X. Qiao); Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A. Osbourn).
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Feng C, Zou S, Gao P, Wang Z. In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit. PeerJ 2021; 9:e12348. [PMID: 34760371 PMCID: PMC8557698 DOI: 10.7717/peerj.12348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/29/2021] [Indexed: 11/23/2022] Open
Abstract
The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.
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Affiliation(s)
- Chen Feng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Shuaiyu Zou
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Puxin Gao
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Zupeng Wang
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.,Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan, China.,Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan, China
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Tiika RJ, Wei J, Ma R, Yang H, Cui G, Duan H, Ma Y. Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit. PeerJ 2020; 8:e10207. [PMID: 33194409 PMCID: PMC7602686 DOI: 10.7717/peerj.10207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background The WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.
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Affiliation(s)
- Richard John Tiika
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China.,Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Jia Wei
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China.,Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Rui Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Yanjun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
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Lu L, Loker ES, Zhang SM, Buddenborg SK, Bu L. Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni. BMC Genomics 2020; 21:190. [PMID: 32122294 PMCID: PMC7053062 DOI: 10.1186/s12864-020-6534-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Background The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansion and loss, and an uncertain functional role, especially in invertebrates. AIGs are frequently represented as GIMAPs (GTPase of the immunity associated protein family), characterized by presence of the AIG1 domain along with coiled-coil domains. Here we provide an overview of the remarkably expanded AIG repertoire of the freshwater gastropod Biomphalaria glabrata, compare it with AIGs in other organisms, and detail patterns of expression in B. glabrata susceptible or resistant to infection with Schistosoma mansoni, responsible for the neglected tropical disease of intestinal schistosomiasis. Results We define the 7 conserved motifs that comprise the AIG1 domain in B. glabrata and detail its association with at least 7 other domains, indicative of functional versatility of B. glabrata AIGs. AIG genes were usually found in tandem arrays in the B. glabrata genome, suggestive of an origin by segmental gene duplication. We found 91 genes with complete AIG1 domains, including 64 GIMAPs and 27 AIG genes without coiled-coils, more than known for any other organism except Danio (with > 100). We defined expression patterns of AIG genes in 12 different B. glabrata organs and characterized whole-body AIG responses to microbial PAMPs, and of schistosome-resistant or -susceptible strains of B. glabrata to S. mansoni exposure. Biomphalaria glabrata AIG genes clustered with expansions of AIG genes from other heterobranch gastropods yet showed unique lineage-specific subclusters. Other gastropods and bivalves had separate but also diverse expansions of AIG genes, whereas cephalopods seem to lack AIG genes. Conclusions The AIG genes of B. glabrata exhibit expansion in both numbers and potential functions, differ markedly in expression between strains varying in susceptibility to schistosomes, and are responsive to immune challenge. These features provide strong impetus to further explore the functional role of AIG genes in the defense responses of B. glabrata, including to suppress or support the development of medically relevant S. mansoni parasites.
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Affiliation(s)
- Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sarah K Buddenborg
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Lijing Bu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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Chouhan OP, Roske Y, Heinemann U, Biswas S. Structure of the active GGEEF domain of a diguanylate cyclase from Vibrio cholerae. Biochem Biophys Res Commun 2019; 523:287-292. [PMID: 31862141 DOI: 10.1016/j.bbrc.2019.11.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 01/05/2023]
Abstract
Cyclic-di-GMP (c-di-GMP) synthesized by diguanylate cyclases has been an important and ubiquitous secondary messenger in almost all bacterial systems. In Vibrio cholerae, c-di-GMP plays an intricate role in the production of the exopolysaccharide matrix, and thereby, in biofilm formation. The formation of the surface biofilm enables the bacteria to survive in aquatic bodies, when not infecting a human host. Diguanylate cyclases are the class of enzymes which synthesize c-di-GMP from two molecules of GTP and are endowed with a GGDEF or, a GGEEF signature domain. The VC0395_0300 protein from V. cholerae, has been established as a diguanylate cyclase with a necessary role in biofilm formation. Here we present the structure of an N-terminally truncated form of VC0395_0300, which retains the active GGEEF domain for diguanylate cyclase activity but lacks 160 residues from the poorly organized N-terminal domain. X-ray diffraction data was collected from a crystal of VC0395_0300(161-321) to a resolution of 1.9 Å. The structure displays remarkable topological similarity with diguanylate cyclases from other bacterial systems, but lacks the binding site for c-di-GMP present in its homologues. Finally, we demonstrate the ability of the truncated diguanylate cyclase VC0395_0300(161-321) to produce c-di-GMP, and its role in biofilm formation for the bacteria.
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Affiliation(s)
| | - Yvette Roske
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Chemistry and Biochemistry Institute, Freie Universität, Berlin, Germany
| | - Sumit Biswas
- ViStA Lab, BITS, Pilani - K K Birla Goa Campus, Zuarinagar, Goa, India.
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Wang X, Liang Y, Fang Z, Huang J, Hong M. The intracellular NPxY motif is critical in maintaining the function and expression of human organic anion transporting polypeptide 1B1. Biochim Biophys Acta Biomembr 2019; 1861:1189-1196. [PMID: 30970235 DOI: 10.1016/j.bbamem.2019.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 10/27/2022]
Abstract
Organic anion transporting polypeptides (OATPs, gene symbol SLCO) mediate sodium-independent transport of endogenous compounds such as bile salts, hormones and their conjugates as well as toxins and drugs. OATP1B1 is the major OATP specifically expressed at the basolateral membrane of human hepatocytes and many clinically important drugs have been shown to be substrates of the transporter. According to the computer-based hydropathy analysis, a large intracellular loop 3 (IL3) is situated between transmembrane domain 6 and 7 of OATPs, in which a conserved NPxY motif is found. In the current study, HEK293 cells expressing the HA-tagged OATP1B1 was utilized to investigate the role of the NPxY motif for the function and expression of the transporter. Alanine replacement of N335 or P336 retained substantial uptake function; while simultaneous mutation of these residues resulted in a double mutant that lost almost all the transport activity. On the other hand, Y338A showed >80% reduction for estrone-3-sulfate uptake. Plasma membrane protein analysis revealed that N335/P336A completely lost its cell surface protein expression; while that of Y338A is dramatically reduced. Further investigation with pharmacological inhibitors and immunocytochemistry demonstrated that N335/336A is detained in the Golgi apparatus and Y338A exhibited accelerated protein degradation rate compared to that of the wild-type. Conservative replacement of Y338 with phenylalanine fully recovered uptake and expression of the transporter. In summary, a new role was observed for the NPxY motif located in the IL3 of OATP1B1, which may affect processing and stability of the transporter.
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Affiliation(s)
- Xuyang Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yushuang Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zihui Fang
- College of Life Sciences, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Jiujiu Huang
- College of Life Sciences, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China.
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Parvathaneni RK, DeLeo VL, Spiekerman JJ, Chakraborty D, Devos KM. Parallel loss of introns in the ABCB1 gene in angiosperms. BMC Evol Biol 2017; 17:238. [PMID: 29202710 PMCID: PMC5716013 DOI: 10.1186/s12862-017-1077-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition. RESULTS An analysis of the ABCB1 gene structure in 80 angiosperms revealed that the number of introns ranged from one to nine. All introns in ABCB1 underwent either a one-time loss (single loss in one lineage/species) or multiple independent losses (parallel loss in two or more lineages/species) with the majority of losses occurring within the grass family. In contrast, the structure of the closest homolog to ABCB1, ABCB19, remained constant in the majority of angiosperms analyzed. Using known phylogenetic relationships within the grasses, we determined the ancestral branch-points where the losses occurred. Intron 7, the longest intron, was lost in only a single species, Mimulus guttatus, following duplication of ABCB1. Semiquantitative PCR showed that the M. guttatus ABCB1 gene copy without intron 7 had significantly lower transcript levels than the gene copy with intron 7. We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. CONCLUSIONS The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. Lack of microhomology in the exon upstream of lost phase I introns was likely due to release of the selective constraint on the penultimate base (3rd base in codon) of the terminal codon by the splicing machinery. In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss.
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Affiliation(s)
- Rajiv K Parvathaneni
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States.,Current address: Donald Danforth Plant Science Center, St. Louis, MO, 63132, United States
| | - Victoria L DeLeo
- Department of Genetics, University of Georgia, 30602, Athens, GA, United States.,Current address: Department of Biology, Pennsylvania State University, University Park, PA, 16802, United States
| | - John J Spiekerman
- Department of Plant Biology, University of Georgia, 30602, Athens, GA, United States
| | - Debkanta Chakraborty
- Institute of Bioinformatics, University of Georgia, 30602, Athens, GA, United States
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States. .,Department of Plant Biology, University of Georgia, 30602, Athens, GA, United States. .,Institute of Bioinformatics, University of Georgia, 30602, Athens, GA, United States.
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Grishaeva TM, Kulichenko D, Bogdanov YF. Bioinformatical analysis of eukaryotic shugoshins reveals meiosis-specific features of vertebrate shugoshins. PeerJ 2016; 4:e2736. [PMID: 27917322 PMCID: PMC5134366 DOI: 10.7717/peerj.2736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/31/2016] [Indexed: 11/24/2022] Open
Abstract
Background Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms. Methods A bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed. Results We identified a C-terminal amino acid motif that is highly evolutionarily conserved among the SGOs protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic SGOs. This meiotic motif is arginine-rich in vertebrates. SGOs differ in different eukaryotic kingdoms by the sets and locations of amino acid motifs and the number of α-helical regions in the protein molecule. Discussion These structural differences between meiotic and mitotic SGOs probably could be responsible for the prolonged SGOs resistance to degradation during meiotic metaphase I and anaphase I. We suggest that the “arginine comb” in C-end meiotic motifs is capable of interaction by hydrogen bonds with guanine bases in the minor groove of DNA helix, thus protecting SGOs from hydrolysis. Our findings support independent evolution of meiosis in different lineages of multicellular organisms.
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Affiliation(s)
- Tatiana M Grishaeva
- Laboratory of Cytogenetics, Department of Genomics and Human Genetics, N.I. Vavilov Institute of General Genetics , Moscow , Russia
| | - Darya Kulichenko
- Laboratory of Cytogenetics, Department of Genomics and Human Genetics, N.I. Vavilov Institute of General Genetics , Moscow , Russia
| | - Yuri F Bogdanov
- Laboratory of Cytogenetics, Department of Genomics and Human Genetics, N.I. Vavilov Institute of General Genetics , Moscow , Russia
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Vatansever R, Filiz E, Ozyigit II. In silico analysis of Mn transporters (NRAMP1) in various plant species. Mol Biol Rep 2016; 43:151-63. [PMID: 26878855 DOI: 10.1007/s11033-016-3950-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 02/09/2016] [Indexed: 01/18/2023]
Abstract
Manganese (Mn) is an essential micronutrient in plant life cycle. It may be involved in photosynthesis, carbohydrate and lipid biosynthesis, and oxidative stress protection. Mn deficiency inhibits the plant growth and development, and causes the various plant symptoms such as interveinal chlorosis and tissue necrosis. Despite its importance in plant life cycle, we still have limited knowledge about Mn transporters in many plant species. Therefore, this study aimed to identify and characterize high affinity Arabidopsis Mn root transporter NRAMP1 orthologs in 17 different plant species. Various in silico methods and digital gene expression data were used in identification and characterization of NRAMP1 homologs; physico-chemical properties of sequences were calculated, putative transmembrane domains (TMDs) and conserved motif signatures were determined, phylogenetic tree was constructed, 3D models and interactome map were generated, and gene expression data was analyzed. 49 NRAMP1 homologs were identified from proteome datasets of 17 plant species using AtNRAMP1 as query. Identified sequences were characterized with a NRAMP domain structure, 10-12 putative TMDs with cytosolic N- and C-terminuses, and 10-14 exons encoding a protein of 500-588 amino acids and 53.8-64.3 kDa molecular weight with basic characteristics. Consensus transport residues, GQSSTITGTYAGQY(/F)V(/I)MQGFLD(/E/N) between TMD-8 and 9 were identified in all sequences but putative N-linked glycosylation sites were not highly conserved. In phylogeny, NRAMP1 sequences demonstrated divergence in lower and higher plants as well as in monocots and dicots. Despite divergence of lower plant Physcomitrella patens in phylogeny, it showed similarity in superposed 3D models. Phylogenetic distribution of AtNRAMP1 and 6 homologs inferred a functional relationship to NRAMP6 sequences in Mn transport, while distribution of OsNRAMP1 and 5 homologs implicated an involvement of NRAMP1 sequences in Mn transport or a cross-talk between in Fe-Mn homeostasis. Interactome analysis further confirmed this cross-talk between Mn and Fe pathways. Gene expression profile of AtNRAMP1 under Fe-, K-, P- and S-deficiencies, and cold, drought, heat and salt stresses revealed various proteins involving in transcription regulation, cofactor biosynthesis, diverse developmental roles, carbohydrate metabolism, oxidation-reduction reactions, cellular signaling and protein degradation pathways. Mn deficiency or toxicity could cause serious adverse effects in plants as well as in humans. To reduce these adversities mainly rely on understanding the molecular mechanisms underlying Mn uptake from the soil. However, we still have limited knowledge regarding the structural and functional roles of Mn transporters in many plant species. Therefore, identification and characterization of Mn root uptake transporter, NRAMP1 orthologs in various plant species will provide valuable theoretical knowledge to better understand Mn transporters as well as it may become an insight for future studies aiming to develop genetically engineered and biofortified plants.
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Chiurillo MA, Cortez DR, Lima FM, Cortez C, Ramírez JL, Martins AG, Serrano MG, Teixeira MM, da Silveira JF. The diversity and expansion of the trans-sialidase gene family is a common feature in Trypanosoma cruzi clade members. Infect Genet Evol 2016; 37:266-74. [PMID: 26640033 DOI: 10.1016/j.meegid.2015.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/21/2015] [Accepted: 11/23/2015] [Indexed: 02/07/2023]
Abstract
Trans-sialidase (TS) is a polymorphic protein superfamily described in members of the protozoan genus Trypanosoma. Of the eight TS groups recently described, TS group I proteins (some of which have catalytic activity) are present in the distantly related Trypanosoma brucei and Trypanosoma cruzi phylogenetic clades, whereas other TS groups have only been described in some species belonging to the T. cruzi clade. In the present study we analyzed the repertoire, distribution and phylogenetic relationships of TS genes among species of the T. cruzi clade based on sequence similarity, multiple sequence alignment and tree-reconstruction approaches using TS sequences obtained with the aid of PCR-based strategies or retrieved from genome databases. We included the following representative isolates of the T. cruzi clade from South America: T. cruzi, T. cruzi Tcbat, Trypanosoma cruzi marinkellei, Trypanosoma dionisii, Trypanosoma rangeli and Trypanosoma conorhini. The cloned sequences encoded conserved TS protein motifs Asp-box and VTVxNVxLYNR but lacked the FRIP motif (conserved in TS group I). The T. conorhini sequences were the most divergent. The hybridization patterns of TS probes with chromosomal bands confirmed the abundance of these sequences in species in the T. cruzi clade. Divergence and relationship analysis placed most of the TS sequences in the groups defined in T. cruzi. Further examination of members of TS group II, which includes T. cruzi surface glycoproteins implicated in host cell attachment and invasion, showed that sequences of T. cruzi Tcbat grouped with those of T. cruzi genotype TcI. Our analysis indicates that different members of the T. cruzi clade, with different vertebrate hosts, vectors and pathogenicity, share the extensive expansion and sequence diversification of the TS gene family. Altogether, our results are congruent with the evolutionary history of the T. cruzi clade and represent a contribution to the understanding of the molecular evolution and role of TS proteins in trypanosomes.
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Yong SYC, Wickneswari R. Molecular characterization of a cellulose synthase gene ( AaxmCesA1) isolated from an Acacia auriculiformis x Acacia mangium hybrid. Plant Mol Biol Report 2013; 31:303-313. [PMID: 24415841 PMCID: PMC3881566 DOI: 10.1007/s11105-012-0499-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cellulose is the major component of plant cell walls, providing mechanical strength to the structural framework of plants. In association with lignin, hemicellulose, protein and pectin, cellulose forms the strong yet flexible bio-composite tissue of wood. Wood formation is an essential biological process and is of significant importance to the cellulosic private sector industry. Cellulose synthase genes encode the catalytic subunits of a large protein complex responsible for the biogenesis of cellulose in higher plants. The hybrid Acacia auriculiformis x Acacia mangium represents an important source of tree cellulose for forest-based product manufacturing, with enormous economic potential. In this work, we isolate the first cellulose synthase gene, designated AaxmCesA1, from this species. The isolated full-length AaxmCesA1 cDNA encodes a polypeptide of 1,064 amino acids. Sequence analyses revealed that AaxmCesA1 cDNA possesses the key motif characteristics of a CesA protein. AaxmCesA1 shares more than 75 % amino acid sequence identity with CesA proteins from other plant species. Subsequently, the full-length AaxmCesA1 gene of 7,389 bp with partial regulatory and 13 intron regions was also isolated. Relative gene expression analysis by quantitative PCR in different tissues of the Acacia hybrid, suggests the involvement of the AaxmCesA1 gene in primary cell wall synthesis of rapidly dividing young root cells. Similarity analyses using Blast algorithms also suggests a role in primary cell wall deposition in the Acacia hybrid. Southern analysis predicts that AaxmCesA1 is a member of a multigene family with at least two isoforms in the genome of the Acacia hybrid.
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Affiliation(s)
- Seok Yien Christina Yong
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan Malaysia
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan Malaysia
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