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Liang Q, Chen N, Wang W, Zhang B, Luo J, Zhong Y, Zhang F, Zhang Z, Martín–Rodríguez AJ, Wang Y, Xiang L, Xiong X, Hu R, Zhou Y. Co-occurrence of ST412 Klebsiella pneumoniae isolates with hypermucoviscous and non-mucoviscous phenotypes in a short-term hospitalized patient. mSystems 2024; 9:e0026224. [PMID: 38904378 PMCID: PMC11265266 DOI: 10.1128/msystems.00262-24] [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: 02/27/2024] [Accepted: 05/10/2024] [Indexed: 06/22/2024] Open
Abstract
Hypermucoviscosity (HMV) is a phenotype that is commonly associated with hypervirulence in Klebsiella pneumoniae. The factors that contribute to the emergence of HMV subpopulations remain unclear. In this study, eight K. pneumoniae strains were recovered from an inpatient who had been hospitalized for 20 days. Three of the isolates exhibited a non-HMV phenotype, which was concomitant with higher biofilm formation than the other five HMV isolates. All eight isolates were highly susceptible to serum killing, albeit HMV strains were remarkably more infective than non-HMV counterparts in a mouse model of infection. Whole genome sequencing (WGS) showed that the eight isolates belonged to the K57-ST412 lineage. Average nucleotide identity (FastANIb) analysis indicated that eight isolates share 99.96% to 99.99% similarity and were confirmed to be the same clone. Through comparative genomics analysis, 12 non-synonymous mutations were found among these isolates, eight of which in the non-HMV variants, including rmpA (c.285delG) and wbaP (c.1305T > A), which are assumed to be associated with the non-HMV phenotype. Mutations in manB (c.1318G > A), dmsB (c.577C > T) and tkt (c.1928C > A) occurred in HMV isolates only. RNA-Seq revealed transcripts of genes involved in energy metabolism, carbohydrate metabolism and membrane transport, including cysP, cydA, narK, tktA, pduQ, aceB, metN, and lsrA, to be significantly dysregulated in the non-HMV strains, suggesting a contribution to HMV phenotype development. This study suggests that co-occurrence of HMV and non-HMV phenotypes in the same clonal population may be mediated by mutational mechanisms as well as by certain genes involved in membrane transport and central metabolism. IMPORTANCE K. pneumoniae with a hypermucoviscosity (HMV) phenotype is a community-acquired pathogen that is associated with increased invasiveness and pathogenicity, and underlying diseases are the most common comorbid risk factors inducing metastatic complications. HMV was earlier attributed to the overproduction of capsular polysaccharide, and more data point to the possibility of several causes contributing to this bacterial phenotype. Here, we describe a unique event in which the same clonal population showed both HMV and non-HMV characteristics. Studies have demonstrated that this process is influenced by mutational processes and genes related to transport and central metabolism. These findings provide fresh insight into the mechanisms behind co-occurrence of HMV and non-HMV phenotypes in monoclonal populations as well as potentially being critical in developing strategies to control the further spread of HMV K. pneumoniae.
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Affiliation(s)
- Qinghua Liang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
- Department of Laboratory Medicine, Yilong County People’s Hospital, Nanchong, China
| | - Nan Chen
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Biying Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Jinjing Luo
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Ying Zhong
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Feiyang Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Alberto J. Martín–Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ying Wang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Li Xiang
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
| | - Xia Xiong
- Department of Dermatology, The Affiliated Hospital,Southwest Medical University, Luzhou, China
| | - Renjing Hu
- Department of Laboratory Medicine, Jiangnan University Medical Center, Wuxi, China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medical, Southwest Medical University, Luzhou, China
- Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medicine University, Luzhou, China
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Li X, Ding M, Wang M, Yang S, Ma X, Hu J, Song F, Wang L, Liang W. Proteome profiling reveals changes in energy metabolism, transport and antioxidation during drought stress in Nostoc flagelliforme. BMC PLANT BIOLOGY 2022; 22:162. [PMID: 35365086 PMCID: PMC8973743 DOI: 10.1186/s12870-022-03542-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 03/18/2022] [Indexed: 05/27/2023]
Abstract
BACKGROUND Drought is an important abiotic stress that constrains the growth of many species. Despite extensive study in model organisms, the underlying mechanisms of drought tolerance in Nostoc flagelliforme remain elusive. RESULTS We characterized the drought adaptation of N. flagelliforme by a combination of proteomics and qRT-PCR. A total of 351 differentially expressed proteins involved in drought stress adaptation were identified. It was found that the expression of several nutrient influx transporters was increased, including molybdate ABC transporter substrate binding protein (modA), sulfate ABC transporter substrate-binding protein (sbp) and nitrate ABC transporter (ntrB), while that of efflux transporters for toxic substances was also increased, including arsenic transporting ATPase (ArsA), potassium transporter (TrkA) and iron ABC transporter substrate-binding protein (VacB). Additionally, photosynthetic components were reduced while sugars built up during drought stress. Non-enzymatic antioxidants, orange carotenoid protein (OCP) homologs, cytochrome P450 (CYP450), proline (Pro) and ascorbic acid (AsA) were all altered during drought stress and may play important roles in scavenging reactive oxygen species (ROS). CONCLUSION In this study, N. flagelliforme may regulates its adaptation to drought stress through the changes of protein expression in photosynthesis, energy metabolism, transport, protein synthesis and degradation and antioxidation. HIGHLIGHTS • A total of 351 DEPs involved in adaptation to drought stress were identified. • Changes in the expression of six OCP homologs were found in response to drought stress. • Differential expression of transporters played an important role in drought stress adaptation. • Most PSII proteins were downregulated, while PSI proteins were unchanged in response to drought stress. • Sugar metabolism was upregulated in response to drought stress.
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Affiliation(s)
- Xiaoxu Li
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Miaomiao Ding
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Meng Wang
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Shujuan Yang
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Xiaorong Ma
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Jinhong Hu
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Fan Song
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Lingxia Wang
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China.
| | - Wenyu Liang
- College of Life Sciences, Ningxia University, Yinchuan, 750021, China.
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Pinto RT, Cardoso TB, Paiva LV, Benedito VA. Genomic and transcriptomic inventory of membrane transporters in coffee: Exploring molecular mechanisms of metabolite accumulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111018. [PMID: 34620453 DOI: 10.1016/j.plantsci.2021.111018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/07/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
The genus Coffea (Rubiaceae) encompasses a group of perennial plant species, including a commodity crop from which seeds are roasted, ground, and infused to make one of the most appreciated beverages in the world. As an important tropical crop restricted to specific regions of the world, coffee production is highly susceptible to the effects of environmental instabilities (i.e., local year-to-year weather fluctuations and global climate change) and threatening pest pressures, not to mention an increasing quality rigor by consumers in industrialized countries. Specialized metabolites are substances that largely affect plant-environment interactions as well as how consumers experience agricultural products. Membrane transporters are key targets, albeit understudied, for understanding and tailoring the spatiotemporal distribution of specialized metabolites as they mediate and control molecular trafficking and substance accumulation. Therefore, we analyzed the transportome of C. canephora encoded within the 25,574 protein-coding genes annotated in the genome of this species and identified 1847 putative membrane transporters. Following, we mined 152 transcriptional profiles of C. canephora and C. arabica and performed a comprehensive co-expression analysis to identify transporters potentially involved in the accumulation of specialized metabolites associated with beverage quality and bioactivity attributes. In toto, this report points to an avenue of possibilities on Coffea genomic and transcriptomic data mining for genetic breeding strategies, which can lead to the development of new, resilient varieties for more sustainable coffee production systems.
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Affiliation(s)
- Renan T Pinto
- Division of Plant and Soil Sciences, West Virginia University, 3425 Agricultural Sciences Building, Morgantown, WV 26506-6108, USA; Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Thiago B Cardoso
- Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Luciano V Paiva
- Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, 3425 Agricultural Sciences Building, Morgantown, WV 26506-6108, USA.
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Abundant Monovalent Ions as Environmental Signposts for Pathogens during Host Colonization. Infect Immun 2021; 89:IAI.00641-20. [PMID: 33526568 DOI: 10.1128/iai.00641-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Host colonization by a pathogen requires proper sensing and response to local environmental cues, to ensure adaptation and continued survival within the host. The ionic milieu represents a critical potential source of environmental cues, and indeed, there has been extensive study of the interplay between host and pathogen in the context of metals such as iron, zinc, and manganese, vital ions that are actively sequestered by the host. The inherent non-uniformity of the ionic milieu also extends, however, to "abundant" ions such as chloride and potassium, whose concentrations vary greatly between tissue and cellular locations, and with the immune response. Despite this, the concept of abundant ions as environmental cues and key players in host-pathogen interactions is only just emerging. Focusing on chloride and potassium, this review brings together studies across multiple bacterial and parasitic species that have begun to define both how these abundant ions are exploited as cues during host infection, and how they can be actively manipulated by pathogens during host colonization. The close links between ion homeostasis and sensing/response to different ionic signals, and the importance of studying pathogen response to cues in combination, are also discussed, while considering the fundamental insight still to be uncovered from further studies in this nascent area of inquiry.
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Geiger D. Plant glucose transporter structure and function. Pflugers Arch 2020; 472:1111-1128. [PMID: 32845347 PMCID: PMC8298354 DOI: 10.1007/s00424-020-02449-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/01/2022]
Abstract
The carbohydrate D-glucose is the main source of energy in living organisms. In contrast to animals, as well as most fungi, bacteria, and archaea, plants are capable to synthesize a surplus of sugars characterizing them as autothrophic organisms. Thus, plants are de facto the source of all food on earth, either directly or indirectly via feed to livestock. Glucose is stored as polymeric glucan, in animals as glycogen and in plants as starch. Despite serving a general source for metabolic energy and energy storage, glucose is the main building block for cellulose synthesis and represents the metabolic starting point of carboxylate- and amino acid synthesis. Finally yet importantly, glucose functions as signalling molecule conveying the plant metabolic status for adjustment of growth, development, and survival. Therefore, cell-to-cell and long-distance transport of photoassimilates/sugars throughout the plant body require the fine-tuned activity of sugar transporters facilitating the transport across membranes. The functional plant counterparts of the animal sodium/glucose transporters (SGLTs) are represented by the proton-coupled sugar transport proteins (STPs) of the plant monosaccharide transporter(-like) family (MST). In the framework of this special issue on “Glucose Transporters in Health and Disease,” this review gives an overview of the function and structure of plant STPs in comparison to the respective knowledge obtained with the animal Na+-coupled glucose transporters (SGLTs).
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Affiliation(s)
- Dietmar Geiger
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, 97082, Wuerzburg, Germany.
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Santos FC, Lobo GM, Fernandes AS, Videira A, de Almeida RFM. Changes in the Biophysical Properties of the Cell Membrane Are Involved in the Response of Neurospora crassa to Staurosporine. Front Physiol 2018; 9:1375. [PMID: 30364194 PMCID: PMC6193110 DOI: 10.3389/fphys.2018.01375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/11/2018] [Indexed: 01/27/2023] Open
Abstract
Neurospora crassa is a non-pathogenic filamentous fungus widely used as a multicellular eukaryotic model. Recently, the biophysical properties of the plasma membrane of N. crassa conidia were thoroughly characterized. They evolve during conidial germination at a speed that depends on culture conditions, suggesting an important association between membrane remodeling and the intense membrane biogenesis that takes place during the germinative process. Staurosporine (STS) is a drug used to induce programmed cell death in various organisms. In N. crassa, STS up-regulates the expression of the ABC transporter ABC-3, which localizes at the plasma membrane and pumps STS out. To understand the role of plasma membrane biophysical properties in the fungal drug response, N. crassa was subjected to STS treatment during early and late conidial development stages. Following 1 h treatment with STS, there is an increase in the abundance of the more ordered, sphingolipid-enriched, domains in the plasma membrane of conidia. This leads to higher fluidity in other membrane regions. The global order of the membrane remains thus practically unchanged. Significant changes in sphingolipid-enriched domains were also observed after 15 min challenge with STS, but they were essentially opposite to those verified for the 1 h treatment, suggesting different types of drug responses. STS effects on membrane properties that are more dependent on ergosterol levels also depend on the developmental stage. There were no alterations on 2 h-grown cells, clearly contrasting to what happens at longer growth times. In this case, the differences were more marked for longer STS treatment, and rationalized considering that the drug prevents the increase in the ergosterol/glycerophospholipid ratio that normally takes place at the late conidial stage/transition to the mycelial stage. This could be perceived as a drug-induced development arrest after 5 h growth, involving ergosterol, and pointing to a role of lipid rafts possibly related with an up-regulated expression of the ABC-3 transporter. Overall, our results suggest the involvement of membrane ordered domains in the response mechanisms to STS in N. crassa.
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Affiliation(s)
- Filipa C Santos
- Departamento de Química e Bioquímica, Faculdade de Ciências, Centro de Química e Bioquímica, Universidade de Lisbon, Campo Grande, Lisbon, Portugal
| | - Gerson M Lobo
- Departamento de Química e Bioquímica, Faculdade de Ciências, Centro de Química e Bioquímica, Universidade de Lisbon, Campo Grande, Lisbon, Portugal
| | - Andreia S Fernandes
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Arnaldo Videira
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Rodrigo F M de Almeida
- Departamento de Química e Bioquímica, Faculdade de Ciências, Centro de Química e Bioquímica, Universidade de Lisbon, Campo Grande, Lisbon, Portugal
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De Biasi MG, Marabottini R, Paolacci AR, Ciaffi M, Nali C, Lorenzini G, Badiani M. On the interactions among zinc availability and responses to ozone stress in durum wheat seedlings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:8181-8189. [PMID: 28994034 DOI: 10.1007/s11356-017-0062-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
Seedlings of durum wheat [Triticum turgidum subsp. durum (Desf.) Husn] were exposed to zinc nutrition and to ozone (O3) in a factorial combination: adequate (+Zn treatment) or no Zn (-Zn) in the nutrient solution, followed by exposure to either ozone-free air (filtered air, FA) or to 150 nL L-1 ozone (O3) for 4 h. Although omitting Zn from the nutrient solution failed to impose a genuine Zn deficiency, -Zn*FA durum wheat seedlings showed a typical deficiency behaviour, i.e. Zn mobilisation from root to shoot. Such inter-organ Zn redistribution, however, did not occur in -Zn*O3 plants. Exposure to each stress singly decreased the activity and the protein amount of foliar plasma membrane H+-ATPase, but not stress combination, which even increased the H+-ATPase expression with respect to control. In the -Zn*O3 plants, moreover, the foliar activities of the plasma membrane-bound NAD(P)H-dependent superoxide synthase and of Cu,Zn-superoxide dismutase, and the transcripts abundance of the luminal binding protein and of the protein disulphide isomerase, were also stimulated. It is proposed that, even in the absence of actual Zn starvation, the perception of deficiency conditions could trigger changes in redox homoeostasis at the plasma membrane level, helpful in compensating an O3-dependent oxidative damage.
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Affiliation(s)
- Margherita G De Biasi
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131, Naples, Italy
| | - Rosita Marabottini
- Dipartimento per l'Innovazione dei Sistemi Biologici, Agroalimentari e Forestali, Università degli Studi della Tuscia, Via S.C. De Lellis, 01100, Viterbo, Italy
| | - Anna Rita Paolacci
- Dipartimento per l'Innovazione dei Sistemi Biologici, Agroalimentari e Forestali, Università degli Studi della Tuscia, Via S.C. De Lellis, 01100, Viterbo, Italy
| | - Mario Ciaffi
- Dipartimento per l'Innovazione dei Sistemi Biologici, Agroalimentari e Forestali, Università degli Studi della Tuscia, Via S.C. De Lellis, 01100, Viterbo, Italy
| | - Cristina Nali
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università degli Studi di Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
| | - Giacomo Lorenzini
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università degli Studi di Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122, Reggio Calabria, Italy.
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Liu T, Li X, Xie S, Wang L, Yang S. RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis. PLANT DIVERSITY 2016; 38:163-170. [PMID: 30159461 PMCID: PMC6112097 DOI: 10.1016/j.pld.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/28/2016] [Accepted: 05/04/2016] [Indexed: 06/08/2023]
Abstract
Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is a rhizomatous, herbaceous, perennial plant that has been used for more than a thousand years in traditional Chinese medicine. It is facing extinction due to overharvesting. Steroids are the major therapeutic components in Paris roots, the commercial value of which increases with age. To date, no genomic data on the species have been available. In this study, transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids. Using Illumina sequencing technology, we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information. Approximately 87,577 unique sequences, with an average length of 614 bases, were obtained from the root cells. Using bioinformatics methods, we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database. The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database. Of 3082 genes that were identified as significantly differentially expressed between roots of different ages, 1518 (49.25%) were upregulated and 1564 (50.75%) were downregulated in the older root. Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids. These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P. polyphylla and facilitate saponin-rich plant development.
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Affiliation(s)
- Tao Liu
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiaoxian Li
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shiqing Xie
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Ling Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Shengchao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
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Haq IU, Graupner K, Nazir R, van Elsas JD. The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled. Genome Biol Evol 2014; 6:1652-68. [PMID: 24923325 PMCID: PMC4122924 DOI: 10.1093/gbe/evu126] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.
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Affiliation(s)
- Irshad Ul Haq
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands
| | - Katharina Graupner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands
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Kumar K, Kumar M, Kim SR, Ryu H, Cho YG. Insights into genomics of salt stress response in rice. RICE (NEW YORK, N.Y.) 2013; 6:27. [PMID: 24280112 PMCID: PMC4883734 DOI: 10.1186/1939-8433-6-27] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Plants, as sessile organisms experience various abiotic stresses, which pose serious threat to crop production. Plants adapt to environmental stress by modulating their growth and development along with the various physiological and biochemical changes. This phenotypic plasticity is driven by the activation of specific genes encoding signal transduction, transcriptional regulation, ion transporters and metabolic pathways. Rice is an important staple food crop of nearly half of the world population and is well known to be a salt sensitive crop. The completion and enhanced annotations of rice genome sequence has provided the opportunity to study functional genomics of rice. Functional genomics aids in understanding the molecular and physiological basis to improve the salinity tolerance for sustainable rice production. Salt tolerant transgenic rice plants have been produced by incorporating various genes into rice. In this review we present the findings and investigations in the field of rice functional genomics that includes supporting genes and networks (ABA dependent and independent), osmoprotectants (proline, glycine betaine, trehalose, myo-inositol, and fructans), signaling molecules (Ca2+, abscisic acid, jasmonic acid, brassinosteroids) and transporters, regulating salt stress response in rice.
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Affiliation(s)
- Kundan Kumar
- />Department of Biological Sciences, Birla Institute of Technology & Science, K. K. Birla Goa Campus, Goa 403726 India
| | - Manu Kumar
- />Department of Life Science, Sogang University, Seoul, 121-742 Korea
| | - Seong-Ryong Kim
- />Department of Life Science, Sogang University, Seoul, 121-742 Korea
| | - Hojin Ryu
- />Department of Life Science, Pohang University of Science & Technology, Pohang, Korea
| | - Yong-Gu Cho
- />Department of Crop Science, Chungbuk National University, Cheongju, 361-763 Korea
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Function and evolution of channels and transporters in photosynthetic membranes. Cell Mol Life Sci 2013; 71:979-98. [PMID: 23835835 PMCID: PMC3928508 DOI: 10.1007/s00018-013-1412-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 05/28/2013] [Accepted: 06/18/2013] [Indexed: 01/21/2023]
Abstract
Chloroplasts from land plants and algae originated from an endosymbiotic event, most likely involving an ancestral photoautotrophic prokaryote related to cyanobacteria. Both chloroplasts and cyanobacteria have thylakoid membranes, harboring pigment-protein complexes that perform the light-dependent reactions of oxygenic photosynthesis. The composition, function and regulation of these complexes have thus far been the major topics in thylakoid membrane research. For many decades, we have also accumulated biochemical and electrophysiological evidence for the existence of solute transthylakoid transport activities that affect photosynthesis. However, research dedicated to molecular identification of the responsible proteins has only recently emerged with the explosion of genomic information. Here we review the current knowledge about channels and transporters from the thylakoid membrane of Arabidopsis thaliana and of the cyanobacterium Synechocystis sp. PCC 6803. No homologues of these proteins have been characterized in algae, although similar sequences could be recognized in many of the available sequenced genomes. Based on phylogenetic analyses, we hypothesize a host origin for most of the so far identified Arabidopsis thylakoid channels and transporters. Additionally, the shift from a non-thylakoid to a thylakoid location appears to have occurred at different times for different transport proteins. We propose that closer control of and provision for the thylakoid by products of the host genome has been an ongoing process, rather than a one-step event. Some of the proteins recruited to serve in the thylakoid may have been the result of the increased specialization of its pigment-protein composition and organization in green plants.
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Pereira MF, de Araújo dos Santos CM, de Araújo EF, de Queiroz MV, Bazzolli DMS. Beginning to understand the role of sugar carriers in Colletotrichum lindemuthianum: the function of the gene mfs1. J Microbiol 2013; 51:70-81. [DOI: 10.1007/s12275-013-2393-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
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Novoa-Aponte L, León-Torres A, Patiño-Ruiz M, Cuesta-Bernal J, Salazar LM, Landsman D, Mariño-Ramírez L, Soto CY. In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex. BMC STRUCTURAL BIOLOGY 2012; 12:25. [PMID: 23031689 PMCID: PMC3573892 DOI: 10.1186/1472-6807-12-25] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 09/27/2012] [Indexed: 12/30/2022]
Abstract
Background P-type ATPases hydrolyze ATP and release energy that is used in the transport of ions against electrochemical gradients across plasma membranes, making these proteins essential for cell viability. Currently, the distribution and function of these ion transporters in mycobacteria are poorly understood. Results In this study, probabilistic profiles were constructed based on hidden Markov models to identify and classify P-type ATPases in the Mycobacterium tuberculosis complex (MTBC) according to the type of ion transported across the plasma membrane. Topology, hydrophobicity profiles and conserved motifs were analyzed to correlate amino acid sequences of P-type ATPases and ion transport specificity. Twelve candidate P-type ATPases annotated in the M. tuberculosis H37Rv proteome were identified in all members of the MTBC, and probabilistic profiles classified them into one of the following three groups: heavy metal cation transporters, alkaline and alkaline earth metal cation transporters, and the beta subunit of a prokaryotic potassium pump. Interestingly, counterparts of the non-catalytic beta subunits of Hydrogen/Potassium and Sodium/Potassium P-type ATPases were not found. Conclusions The high content of heavy metal transporters found in the MTBC suggests that they could play an important role in the ability of M. tuberculosis to survive inside macrophages, where tubercle bacilli face high levels of toxic metals. Finally, the results obtained in this work provide a starting point for experimental studies that may elucidate the ion specificity of the MTBC P-type ATPases and their role in mycobacterial infections.
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Affiliation(s)
- Lorena Novoa-Aponte
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia, Carrera 30 # 45–03, Ciudad Universitaria, Bogotá, Colombia
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Aranda-Sicilia MN, Cagnac O, Chanroj S, Sze H, Rodríguez-Rosales MP, Venema K. Arabidopsis KEA2, a homolog of bacterial KefC, encodes a K(+)/H(+) antiporter with a chloroplast transit peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2362-71. [PMID: 22551943 DOI: 10.1016/j.bbamem.2012.04.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/10/2012] [Accepted: 04/16/2012] [Indexed: 01/10/2023]
Abstract
KEA genes encode putative K(+) efflux antiporters that are predominantly found in algae and plants but are rare in metazoa; however, nothing is known about their functions in eukaryotic cells. Plant KEA proteins show homology to bacterial K(+) efflux (Kef) transporters, though two members in the Arabidopsis thaliana family, AtKEA1 and AtKEA2, have acquired an extra hydrophilic domain of over 500 residues at the amino terminus. We show that AtKEA2 is highly expressed in leaves, stems and flowers, but not in roots, and that an N-terminal peptide of the protein is targeted to chloroplasts in Arabidopsis cotyledons. The full-length AtKEA2 protein was inactive when expressed in yeast; however, a truncated AtKEA2 protein (AtsKEA2) lacking the N-terminal domain complemented disruption of the Na(+)(K(+))/H(+) antiporter Nhx1p to confer hygromycin resistance and tolerance to Na(+) or K(+) stress. To test transport activity, purified truncated AtKEA2 was reconstituted in proteoliposomes containing the fluorescent probe pyranine. Monovalent cations reduced an imposed pH gradient (acid inside) indicating AtsKEA2 mediated cation/H(+) exchange with preference for K(+)=Cs(+)>Li(+)>Na(+). When a conserved Asp(721) in transmembrane helix 6 that aligns to the cation binding Asp(164) of Escherichia coli NhaA was replaced with Ala, AtsKEA2 was completely inactivated. Mutation of a Glu(835) between transmembrane helix 8 and 9 in AtsKEA2 also resulted in loss of activity suggesting this region has a regulatory role. Thus, AtKEA2 represents the founding member of a novel group of eukaryote K(+)/H(+) antiporters that modulate monovalent cation and pH homeostasis in plant chloroplasts or plastids.
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Spetea C, Schoefs B. Solute transporters in plant thylakoid membranes: Key players during photosynthesis and light stress. Commun Integr Biol 2011; 3:122-9. [PMID: 20585503 DOI: 10.4161/cib.3.2.10909] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 12/09/2009] [Indexed: 11/19/2022] Open
Abstract
Plants utilize sunlight to drive photosynthetic energy conversion in the chloroplast thylakoid membrane. Here are located four major photosynthetic complexes, about which we have great knowledge in terms of structure and function. However, much less we know about auxiliary proteins, such as transporters, ensuring an optimum function and turnover of these complexes. The most prominent thylakoid transporter is the proton-translocating ATP-synthase. Recently, four additional transporters have been identified in the thylakoid membrane of Arabidopsis thaliana, namely one copper-transporting P-ATPase, one chloride channel, one phosphate transporter, and one ATP/ADP carrier. Here, we review the current knowledge on the function and physiological role of these transporters during photosynthesis and light stress in plants. Subsequently, we make a survey on the outlook of thylakoid activities awaiting identification of responsible proteins. Such knowledge is necessary to understand the thylakoid network of transporters, and to design strategies for bioengineering crop plants in the future.
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Jha A, Joshi M, Yadav NS, Agarwal PK, Jha B. Cloning and characterization of the Salicornia brachiata Na(+)/H(+) antiporter gene SbNHX1 and its expression by abiotic stress. Mol Biol Rep 2011; 38:1965-73. [PMID: 20853145 DOI: 10.1007/s11033-010-0318-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
Salinity causes multifarious adverse effects to plants. Plants response to salt stress involves numerous processes that function in coordination to alleviate both cellular hyperosmolarity and ion disequilibrium. A Na(+)/H(+) antiporter NHX1 gene has been isolated from a halophytic plant Salicornia brachiata in this study. Predicted amino acid sequence similarity, protein topology and the presence of functional domains conserved in SbNHX1 classify it as a plant vacuolar NHX gene. The SbNHX1 cDNA has an open reading frame of 1,683 bp, encoding a polypeptide of 560 amino acid residues with an estimated molecular mass 62.44 kDa. The SbNHX1 shows high amino acid similarity with other halophytic NHX gene and belongs to Class-I type NHXs. TMpred suggests that SbNHX1 contains 11 strong transmembrane (TM). Real time PCR analysis revealed that SbNHX1 transcript expresses maximum at 0.5 M. Transcript increases gradually by increasing the treatment duration at 0.5 M NaCl, however, maximum expression was observed at 48 h. The overexpression of SbNHX1 gene in tobacco plant showed NaCl tolerance. This study shows that SbNHX1 is a potential gene for salt tolerance, and can be used in future for developing salt tolerant crops.
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Affiliation(s)
- Anupama Jha
- Discipline of Marine Biotechnology and Ecology, Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research, Bhavnagar, 364 002 Gujarat, India
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Conte SS, Lloyd AM. Exploring multiple drug and herbicide resistance in plants--spotlight on transporter proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:196-203. [PMID: 21421361 DOI: 10.1016/j.plantsci.2010.10.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/18/2010] [Accepted: 10/28/2010] [Indexed: 05/23/2023]
Abstract
Multiple drug resistance (MDR) has been extensively studied in bacteria, yeast, and mammalian cells due to the great clinical significance of this problem. MDR is not well studied in plant systems, although plant genomes contain large numbers of genes encoding putative MDR transporters (MDRTs). Biochemical pathways in the chloroplast are the targets of many herbicides and antibiotics, yet very little data is available regarding mechanisms of drug transport across the chloroplast membrane. MDRTs typically have broad substrate specificities, and may transport essential compounds and metabolites in addition to toxins. Indeed, plant transporters belonging to MDR families have also been implicated in the transport of a wide variety of compounds including auxins, flavonoids, glutathione conjugates, metal chelators, herbicides and antibiotics, although definitive evidence that a single transporter is capable of moving both toxins and metabolites has not yet been provided. Current understanding of plant MDR can be expanded via the characterization of candidate genes, especially MDRTs predicted to localize to the chloroplast, and also via traditional forward genetic approaches. Novel plant MDRTs have the potential to become endogenous selectable markers, aid in phytoremediation strategies, and help us to understand how plants have evolved to cope with toxins in their environment.
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Affiliation(s)
- Sarah S Conte
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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Qi H, Chen H, Ao J, Zhou H, Chen X. Identification of differentially expressed genes in Sulfobacillus sp. TPY grown on either elemental sulphur or Fe(2+). J GEN APPL MICROBIOL 2011; 56:389-97. [PMID: 21099135 DOI: 10.2323/jgam.56.389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sulfobacillus sp. TPY is a moderately thermophilic and acidophilic bacterium found in hydrothermal vents in the Pacific Ocean. This bacterium can oxidize ferrous sulfate (Fe(2+)) and elemental sulfur (S(0)) under separate conditions. We used random arbitrarily primed polymerase chain reaction (RAP-PCR) to screen and identify differentially expressed genes from bacteria grown on Fe(2+) or S(0) as the energy source. Fifty-five differential cDNA fragments were isolated and subjected to single-pass sequencing. Thirty-five fragments were identified as orthologs of known genes in the GenBank databases, of which 19 were confirmed to be differentially expressed at the transcriptional level by Northern blot analysis. Among these 19 genes, 14 genes, including isocitrate dehydrogenase, formyltetrahydrofolate deformylase, 3-hydroxybutyryl-CoA dehydrogenase, and GTP-binding protein, were upregulated in TPY grown on Fe(2+) or downregulated in TPY grown on S(0), while five genes such as the outer membrane adhesion-like protein, phosphomannomutase, and cysteine desulfurase sufS were upregulated in TPY strain grown on S(0) or downregulated in TPY grown on Fe(2+). These altered genes are involved in metabolism, osmotic stress, cell membrane alterations, oxidative stress, and the regulatory adaptive response. These results will aid our understanding of the molecular basis of Fe(2+) or S(0) oxidation by the moderately thermophilic and acidophilic bacteria.
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Affiliation(s)
- Huizhou Qi
- Laboratory of Marine Biogenetic Resources of State Oceanic Administration, Third Institute of Oceanography, Fujian, People's Republic of China
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Microbial excavation of solid carbonates powered by P-type ATPase-mediated transcellular Ca2+ transport. Proc Natl Acad Sci U S A 2010; 107:21749-54. [PMID: 21115827 DOI: 10.1073/pnas.1011884108] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Some microbes, among them a few species of cyanobacteria, are able to excavate carbonate minerals, from limestone to biogenic carbonates, including coral reefs, in a bioerosive activity that directly links biological and geological parts of the global carbon cycle. The physiological mechanisms that enable such endolithic cyanobacteria to bore, however, remain unknown. In fact, their boring constitutes a geochemical paradox, in that photoautotrophic metabolism will tend to precipitate carbonates, not dissolve them. We developed a stable microbe/mineral boring system based on a cyanobacterial isolate, strain BC008, with which to study the process of microbial excavation directly in the laboratory. Measurements of boring into calcite under different light regimes, and an analysis of photopigment content and photosynthetic rates along boring filaments, helped us reject mechanisms based on the spatial or temporal separation of alkali versus Acid-generating metabolism (i.e., photosynthesis and respiration). Instead, extracellular Ca(2+) imaging of boring cultures in vivo showed that BC008 was able to take up Ca(2+) at the excavation front, decreasing the local extracellular ion activity product of calcium carbonate enough to promote spontaneous dissolution there. Intracellular Ca(2+) was then transported away along the multicellular cyanobacterial trichomes and excreted at the distal borehole opening into the external medium. Inhibition assays and gene expression analyses indicate that the uptake and transport was driven by P-type Ca(2+)-ATPases. We believe such a chemically simple and biologically sophisticated mechanism for boring to be unparalleled among bacteria.
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Wanke D, Kolukisaoglu HU. An update on the ABCC transporter family in plants: many genes, many proteins, but how many functions? PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12 Suppl 1:15-25. [PMID: 20712617 DOI: 10.1111/j.1438-8677.2010.00380.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ABCC subfamily of the ATP binding cassette (ABC) transporters, which were formerly known as multidrug resistance-related proteins (MRPs), consists of closely related members found in all eukaryotic organisms. Although more than a decade of intensive research has elapsed since the first MRP protein was functionally characterised in Arabidopsis thaliana, knowledge of this particular transporter family is still limited in plants. Although ABCC proteins were originally defined as vacuolar pumps of glutathione-S (GS) conjugates, evidence, as well as speculation, on their endogenous functions inside the cell ranges from detoxification and heavy metal sequestration, to chlorophyll catabolite transport and ion channel regulation. The characterisation of knockout mutants in Arabidopsis has been pivotal for elucidation of different roles of ABCC transporters. However, a functional annotation for the majority of these transport proteins is still lacking, even in this model plant. On the one hand, this problem seems to be caused by functional redundancy between family members, which might lead to physiological complementation by a highly homologous gene in the mutant lines. On the other hand, there is growing evidence that the functional diversity of ABCC genes in Arabidopsis and other plants is far greater than previously assumed. For example, analysis of microarray expression data supports involvement of ABCC transporters in the response to biotic stress: particular changes in ABCC transcript levels are found, which are pathogen-specific and evoke distinct signalling cascades. Current knowledge about plant ABCC transporters indicates that novel and unexpected functions and substrates of these proteins are still waiting to be elucidated.
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Affiliation(s)
- D Wanke
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
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Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mandal MK, Chakraborty N, Datta A, Chakraborty S. Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 2009; 10:415. [PMID: 19732460 PMCID: PMC2755012 DOI: 10.1186/1471-2164-10-415] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 09/05/2009] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on Fusarium wilt responsive gene expression in chickpea. RESULTS We report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a CaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome. CONCLUSION Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of CaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.
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Affiliation(s)
- Nasheeman Ashraf
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Deepali Ghai
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pranjan Barman
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Swaraj Basu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Nagaraju Gangisetty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mihir K Mandal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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