scispace - formally typeset
Search or ask a question
Author

Jitendra P. Khurana

Bio: Jitendra P. Khurana is an academic researcher from University of Delhi. The author has contributed to research in topics: Arabidopsis & Gene. The author has an hindex of 43, co-authored 152 publications receiving 7819 citations. Previous affiliations of Jitendra P. Khurana include International Centre for Genetic Engineering and Biotechnology.
Topics: Arabidopsis, Gene, Genome, Oryza sativa, Auxin


Papers
More filters
Journal ArticleDOI
TL;DR: The expression of UBQ5 and eEF-1alpha was most stable across all the tissue samples examined, however, 18S and 25S rRNA exhibited most stable expression in plants grown under various environmental conditions.

1,061 citations

Journal ArticleDOI
TL;DR: In this paper, the basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes and are also involved in stress and hormone signaling.
Abstract: The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.

453 citations

01 Jan 2008
TL;DR: The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development and differential expression patterns in rice seedlings in response to abiotic stress and light irradiation.
Abstract: The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.

416 citations

Journal ArticleDOI
Tsuyoshi Tanaka1, Baltazar A. Antonio1, Shoshi Kikuchi1, Takashi Matsumoto1, Yoshiaki Nagamura1, Hisataka Numa1, Hiroaki Sakai1, Jianzhong Wu1, Takeshi Itoh2, Takeshi Itoh1, Takuji Sasaki1, Ryo Aono, Yasuyuki Fujii3, Takuya Habara, Erimi Harada, Masako Kanno, Yoshihiro Kawahara4, Hiroaki Kawashima, Hiromi Kubooka, Akihiro Matsuya, Hajime Nakaoka, Naomi Saichi, Ryoko Sanbonmatsu, Yoshiharu Sato, Yuji Shinso, Mami Suzuki, Jun-ichi Takeda, Motohiko Tanino, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Chisato Yamasaki, Tadashi Imanishi2, Toshihisa Okido, Masahito Tada, Kazuho Ikeo, Yoshio Tateno, Takashi Gojobori, Yao-Cheng Lin5, Fu Jin Wei5, Yue-Ie C. Hsing5, Qiang Zhao, Bin Han, Melissa Kramer6, Richard W. McCombie6, David Lonsdale7, Claire O'Donovan7, Eleanor J. Whitfield7, Rolf Apweiler7, Kanako O. Koyanagi8, Jitendra P. Khurana9, Saurabh Raghuvanshi9, Nagendra K. Singh10, Akhilesh K. Tyagi9, Georg Haberer, Masaki Fujisawa, Satomi Hosokawa, Yukiyo Ito, Hiroshi Ikawa, Michie Shibata, Mayu Yamamoto, Richard Bruskiewich11, Douglas R. Hoen12, Thomas E. Bureau12, Nobukazu Namiki13, Hajime Ohyanagi13, Yasumichi Sakai13, Satoshi Nobushima13, Katsumi Sakata13, Roberto A. Barrero14, Yutaka Sato15, Alexandre Souvorov16, Brian Smith-White16, Tatiana Tatusova16, Suyoung An17, Gynheung An17, Satoshi Oota, Galina Fuks18, Joachim Messing, Karen R. Christie19, Damien Lieberherr20, Hyeran Kim21, Andrea Zuccolo21, Rod A. Wing, Kan Nobuta22, Pamela J. Green22, Cheng Lu22, Blake C. Meyers22, Cristian Chaparro23, Benoît Piégu23, Olivier Panaud23, Manuel Echeverria23 
TL;DR: The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc.
Abstract: The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

342 citations

Journal ArticleDOI
TL;DR: Microarray analysis of auxin‐responsive genes in rice revealed that genes involved in various biological processes, including metabolism, transcription, signal transduction, and transport, are regulated by auxin.
Abstract: Auxin influences growth and development in plants by altering gene expression. Many auxin-responsive genes have been characterized in Arabidopsis in detail, but not in crop plants. Earlier, we reported the identification and characterization of the members of the GH3, Aux/IAA and SAUR gene families in rice. In this study, whole genome microarray analysis of auxin-responsive genes in rice was performed, with the aim of gaining some insight into the mechanism of auxin action. A comparison of expression profiles of untreated and auxin-treated rice seedlings identified 315 probe sets representing 298 (225 upregulated and 73 downregulated) unique genes as auxin-responsive. Functional categorization revealed that genes involved in various biological processes, including metabolism, transcription, signal transduction, and transport, are regulated by auxin. The expression profiles of auxin-responsive genes identified in this study and those of the members of the GH3, Aux/IAA, SAUR and ARF gene families were analyzed during various stages of vegetative and reproductive (panicle and seed) development by employing microarray analysis. Many of these genes are, indeed, expressed in a tissue-specific or developmental stage-specific manner, and the expression profiles of some of the representative genes were confirmed by real-time PCR. The differential expression of auxin-responsive genes during various stages of panicle and seed development implies their involvement in diverse developmental processes. Moreover, several auxin-responsive genes were differentially expressed under various abiotic stress conditions, indicating crosstalk between auxin and abiotic stress signaling.

340 citations


Cited by
More filters
Journal ArticleDOI

3,734 citations

Journal ArticleDOI
29 Jan 2009-Nature
TL;DR: An initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome is presented, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information.
Abstract: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

2,809 citations

Journal ArticleDOI
Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu  +320 moreInstitutions (51)
31 May 2012-Nature
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

2,687 citations

Journal ArticleDOI
TL;DR: In this article, the experimental amenability of yeast as a unicellular model system has enabled the discovery of multiple sugar sensors and signaling pathways, and a central role for hexokinase (HXK) as conserved glucose sensor.
Abstract: Sugars not only fuel cellular carbon and energy metabolism but also play pivotal roles as signaling molecules. The experimental amenability of yeast as a unicellular model system has enabled the discovery of multiple sugar sensors and signaling pathways. In plants, different sugar signals are generated by photosynthesis and carbon metabolism in source and sink tissues to modulate growth, development, and stress responses. Genetic analyses have revealed extensive interactions between sugar and plant hormone signaling, and a central role for hexokinase (HXK) as a conserved glucose sensor. Diverse sugar signals activate multiple HXK-dependent and HXKindependent pathways and use different molecular mechanisms to control transcription, translation, protein stability and enzymatic activity. Important and complex roles for Snf1-related kinases (SnRKs), extracellular sugar sensors, and trehalose metabolism in plant sugar signaling are now also emerging.

1,983 citations

Journal ArticleDOI
TL;DR: The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
Abstract: The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

1,834 citations