Publications by category
Journal articles
Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal JJ, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, et al (2023). 25 Years of thermomorphogenesis research: milestones and perspectives. Trends in Plant Science
Gaillochet C, Burko Y, Platre MP, Zhang L, Simura J, Willige BC, Kumar SV, Ljung K, Chory J, Busch W, et al (2020). HY5 and phytochrome activity modulate shoot-to-root coordination during thermomorphogenesis in Arabidopsis.
Development,
147(24).
Abstract:
HY5 and phytochrome activity modulate shoot-to-root coordination during thermomorphogenesis in Arabidopsis.
Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. Although the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here, we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development in Arabidopsis a shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintaining auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Taken together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.
Abstract.
Author URL.
Bouré N, Kumar SV, Arnaud N (2019). The BAP Module: a Multisignal Integrator Orchestrating Growth.
Trends in Plant Science,
24(7), 602-610.
Abstract:
The BAP Module: a Multisignal Integrator Orchestrating Growth
Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.
Abstract.
Gangappa SN, Kumar SV (2018). DET1 and COP1 Modulate the Coordination of Growth and Immunity in Response to Key Seasonal Signals in Arabidopsis.
Cell Reports,
25(1), 29-37.e3.
Abstract:
DET1 and COP1 Modulate the Coordination of Growth and Immunity in Response to Key Seasonal Signals in Arabidopsis
Plant growth and development and outcomes of plant-microbe interactions are defined by coordinated responses to seasonal signals. The mechanisms that control the coordinated regulation of growth and immunity are not well understood. Here, we show that a common signaling module integrates environmental signals, such as photoperiod and temperature, to regulate the growth-defense balance. Key light-signaling components De-Etiolated 1 (DET1) and Constitutive Photomorphogenic 1 (COP1) negatively regulate immunity and are essential for immune modulation by photoperiod and temperature. Our results show that this is regulated by the transcription factor Phytochrome Interacting Factor 4 (PIF4), suggesting that the DET1/COP1-PIF4 module acts as a central hub for the control of growth and immunity in response to seasonal signals. These findings provide a regulatory framework for environmental signal integration. In plants, adaptive traits such as growth and immunity are strongly influenced by the environment. How multiple seasonal signals are integrated is not well understood. Gangappa and Kumar show that a common signaling module comprising DET1, COP1, and PIF4 coordinates growth and immunity in response to key seasonal signals.
Abstract.
Kumar SV (2018). H2A.Z at the Core of Transcriptional Regulation in Plants. Molecular Plant, 11(9), 1112-1114.
Li X-R, Deb J, Kumar SV, Ostergaard L (2018). Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae.
MOLECULAR PLANT,
11(4), 598-606.
Author URL.
Gangappa SN, Kumar SV (2017). DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms.
CELL REPORTS,
18(2), 344-351.
Author URL.
Gangappa SN, Berriri S, Kumar SV (2017). PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis.
CURRENT BIOLOGY,
27(2), 243-249.
Author URL.
Yu N, Nuetzmann H-W, MacDonald JT, Moore B, Field B, Berriri S, Trick M, Rosser SJ, Kumar SV, Freemont PS, et al (2016). Delineation of metabolic gene clusters in plant genomes by chromatin signatures.
NUCLEIC ACIDS RESEARCH,
44(5), 2255-2265.
Author URL.
Berriri S, Gangappa SN, Kumar SV (2016). SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis.
MOLECULAR PLANT,
9(7), 1051-1065.
Author URL.
Gardener C, Kumar SV (2015). Hot n' Cold: Molecular Signatures of Domestication Bring Fresh Insights into Environmental Adaptation.
MOLECULAR PLANT,
8(10), 1439-1441.
Author URL.
Kumar SV, Lucyshyn D, Jaeger KE, Alos E, Alvey E, Harberd NP, Wigge PA (2012). Transcription factor PIF4 controls the thermosensory activation of flowering.
NATURE,
484(7393), 242-U127.
Author URL.
Franklin KA, Lee SH, Patel D, Kumar SV, Spartz AK, Gu C, Ye S, Yu P, Breen G, Cohen JD, et al (2011). PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,
108(50), 20231-20235.
Author URL.
Kumar SV, Wigge PA (2010). H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis.
CELL,
140(1), 136-147.
Author URL.
Kumar V, Wigge PA (2007). Red sky in the morning, shepherd's warning. Nature Genetics, 39(11), 1309-1310.
Rajam MV, Kumar SV (2006). Green Alga (Chlamydomonas reinhardtii).
Methods Mol Biol,
344, 421-433.
Abstract:
Green Alga (Chlamydomonas reinhardtii).
This protocol describes the Agrobacterium tumefaciens-mediated nuclear transformation of a microalgae Chlamydomonas reinhardtii, using a gene construct carrying the genes coding for beta-glucuronidase (gus), green fluorescent protein (gfp), and hygromycin phosphotransferase (hpt). The transformation frequency with this protocol as revealed by hygromycin resistance was many fold higher (about 50-fold) than that of the commonly used glass bead method of transformation. The simplicity of Agrobacterium-mediated gene transfer and the high transformation frequency as well as the precision of T-DNA integration will enable further molecular dissection of this important model organism as well as other algal systems to understand basic plant metabolic processes as well as to exploit the systems for biotechnological applications.
Abstract.
Author URL.
Kumar SV, Basu B, Rajam MV (2006). Modulation of polyamine levels influence growth and cell division in Chlamydomonas reinhardtii.
Physiology and Molecular Biology of Plants,
12(1), 53-58.
Abstract:
Modulation of polyamine levels influence growth and cell division in Chlamydomonas reinhardtii
We report the influence of altered polyamine levels on the growth and cell division in the unicellular green alga Chlamydomonas reinhardtii. Polyamine levels in cells were modulated by exogenous addition of polyamines and their inhibitors. PUT and SPD treatments resulted in an increased cell division and the occurrence of high frequency multiple divisions as well as the impairment of flagella formation, which was correlated with increased levels of the respective polyamines. SPM treatment has been cytotoxic. Polyamine analysis has revealed that the SPM treated cells were depleted of SPD, a possible cause of lethality. Transgenic lines of Chlamydomonas with the polyamine biosynthesis genes adc, odc and samdc were generated to study the influence of transgene over-expression and consequent metabolic alterations. Surprisingly, transgenic lines did not show any change in polyamine levels, which can be attributed to inefficient transgene expression or codon bias. Results from the experiments underline the importance of polyamines in growth and development.
Abstract.
Kumar SV, Rajam MV (2005). Polyamines enhance Agrobacterium tumefaciens vir gene induction and T-DNA transfer.
PLANT SCIENCE,
168(2), 475-480.
Author URL.
Narula A, Kumr SV, Pande D, Rajam MV, Srivastava PS (2004). Agrobacterium-mediated transfer of arginine decarboxylase and ornithine decarboxylase genes to Datura innoxia enhances shoot regeneration and hyoscyamine biosynthesis.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY,
13(2), 127-130.
Author URL.
Kumar SV, Misquitta RW, Reddy VS, Rao BJ, Rajam MV (2004). Genetic transformation of the green alga - Chlamydomonas reinhardtii by Agrobacterium tumefaciens.
PLANT SCIENCE,
166(3), 731-738.
Author URL.
Kumar SV, Rajam MV (2004). Polyamine-ethylene nexus: a potential target for post-harvest biotechnology.
Indian Journal of Biotechnology,
3(2), 299-304.
Abstract:
Polyamine-ethylene nexus: a potential target for post-harvest biotechnology
Post-harvest biotechnology is a fast growing field of plant biotechnology. Achievements were made in the field to delay or prevent fruit ripening and softening by genetic manipulation of ethylene and cell wall metabolism. Despite the development of transgenic plants with the desired traits, the technology has not achieved the pace due to drawbacks of the existing strategies to effectively control the developmental processes following harvest. Here the authors analyse various strategies of post-harvest biotechnology and prospects, giving special emphasis to the metabolic interactions of pathways related to post-harvest characteristics-those of polyamine and ethylene-and the engineering of polyamine metabolism as an alternate strategy for post-harvest biotechnology by carefully manipulating the delicate metabolic balance and the benefits of the newly proposed strategy over the currently used ones.
Abstract.
Kashyap V, Vinod Kumar S, Collonnier C, Fusari F, Haicour R, Rotino GL, Sihachakr D, Rajam MV (2003). Biotechnology of eggplant. Scientia Horticulturae, 97(1), 1-25.
Chapters
Kumar SV, Lucyshyn D (2017). Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP). In (Ed)
, 193-203.
Abstract:
Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP).
Abstract.
Author URL.
Rajam MV, Kumar SV (2007). Eggplant. In (Ed) Biotechnology in Agriculture and Forestry, 201-219.
Publications by year
2023
Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal JJ, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, et al (2023). 25 Years of thermomorphogenesis research: milestones and perspectives. Trends in Plant Science
2020
Gaillochet C, Burko Y, Platre MP, Zhang L, Simura J, Willige BC, Kumar SV, Ljung K, Chory J, Busch W, et al (2020). HY5 and phytochrome activity modulate shoot-to-root coordination during thermomorphogenesis in Arabidopsis.
Development,
147(24).
Abstract:
HY5 and phytochrome activity modulate shoot-to-root coordination during thermomorphogenesis in Arabidopsis.
Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. Although the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here, we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development in Arabidopsis a shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintaining auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Taken together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.
Abstract.
Author URL.
2019
Bouré N, Kumar SV, Arnaud N (2019). The BAP Module: a Multisignal Integrator Orchestrating Growth.
Trends in Plant Science,
24(7), 602-610.
Abstract:
The BAP Module: a Multisignal Integrator Orchestrating Growth
Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.
Abstract.
2018
Gangappa SN, Kumar SV (2018). DET1 and COP1 Modulate the Coordination of Growth and Immunity in Response to Key Seasonal Signals in Arabidopsis.
Cell Reports,
25(1), 29-37.e3.
Abstract:
DET1 and COP1 Modulate the Coordination of Growth and Immunity in Response to Key Seasonal Signals in Arabidopsis
Plant growth and development and outcomes of plant-microbe interactions are defined by coordinated responses to seasonal signals. The mechanisms that control the coordinated regulation of growth and immunity are not well understood. Here, we show that a common signaling module integrates environmental signals, such as photoperiod and temperature, to regulate the growth-defense balance. Key light-signaling components De-Etiolated 1 (DET1) and Constitutive Photomorphogenic 1 (COP1) negatively regulate immunity and are essential for immune modulation by photoperiod and temperature. Our results show that this is regulated by the transcription factor Phytochrome Interacting Factor 4 (PIF4), suggesting that the DET1/COP1-PIF4 module acts as a central hub for the control of growth and immunity in response to seasonal signals. These findings provide a regulatory framework for environmental signal integration. In plants, adaptive traits such as growth and immunity are strongly influenced by the environment. How multiple seasonal signals are integrated is not well understood. Gangappa and Kumar show that a common signaling module comprising DET1, COP1, and PIF4 coordinates growth and immunity in response to key seasonal signals.
Abstract.
Kumar SV (2018). H2A.Z at the Core of Transcriptional Regulation in Plants. Molecular Plant, 11(9), 1112-1114.
Li X-R, Deb J, Kumar SV, Ostergaard L (2018). Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae.
MOLECULAR PLANT,
11(4), 598-606.
Author URL.
2017
Gangappa SN, Kumar SV (2017). DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms.
CELL REPORTS,
18(2), 344-351.
Author URL.
Gangappa SN, Berriri S, Kumar SV (2017). PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis.
CURRENT BIOLOGY,
27(2), 243-249.
Author URL.
Kumar SV, Lucyshyn D (2017). Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP). In (Ed)
, 193-203.
Abstract:
Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP).
Abstract.
Author URL.
2016
Yu N, Nuetzmann H-W, MacDonald JT, Moore B, Field B, Berriri S, Trick M, Rosser SJ, Kumar SV, Freemont PS, et al (2016). Delineation of metabolic gene clusters in plant genomes by chromatin signatures.
NUCLEIC ACIDS RESEARCH,
44(5), 2255-2265.
Author URL.
Berriri S, Gangappa SN, Kumar SV (2016). SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis.
MOLECULAR PLANT,
9(7), 1051-1065.
Author URL.
2015
Gardener C, Kumar SV (2015). Hot n' Cold: Molecular Signatures of Domestication Bring Fresh Insights into Environmental Adaptation.
MOLECULAR PLANT,
8(10), 1439-1441.
Author URL.
2012
Kumar SV, Lucyshyn D, Jaeger KE, Alos E, Alvey E, Harberd NP, Wigge PA (2012). Transcription factor PIF4 controls the thermosensory activation of flowering.
NATURE,
484(7393), 242-U127.
Author URL.
2011
Wigge PA, Kumar SV (2011). METHODS AND COMPOSITIONS FOR ALTERING TEMPERATURE SENSING IN EUKARYOTIC ORGANISMS.
Franklin KA, Lee SH, Patel D, Kumar SV, Spartz AK, Gu C, Ye S, Yu P, Breen G, Cohen JD, et al (2011). PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,
108(50), 20231-20235.
Author URL.
Wigge PA, Kumar SV (2011). Temperature Sensing in Plants.
2010
Kumar SV, Wigge PA (2010). H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis.
CELL,
140(1), 136-147.
Author URL.
2007
Rajam MV, Kumar SV (2007). Eggplant. In (Ed) Biotechnology in Agriculture and Forestry, 201-219.
Kumar V, Wigge PA (2007). Red sky in the morning, shepherd's warning. Nature Genetics, 39(11), 1309-1310.
2006
Rajam MV, Kumar SV (2006). Green Alga (Chlamydomonas reinhardtii).
Methods Mol Biol,
344, 421-433.
Abstract:
Green Alga (Chlamydomonas reinhardtii).
This protocol describes the Agrobacterium tumefaciens-mediated nuclear transformation of a microalgae Chlamydomonas reinhardtii, using a gene construct carrying the genes coding for beta-glucuronidase (gus), green fluorescent protein (gfp), and hygromycin phosphotransferase (hpt). The transformation frequency with this protocol as revealed by hygromycin resistance was many fold higher (about 50-fold) than that of the commonly used glass bead method of transformation. The simplicity of Agrobacterium-mediated gene transfer and the high transformation frequency as well as the precision of T-DNA integration will enable further molecular dissection of this important model organism as well as other algal systems to understand basic plant metabolic processes as well as to exploit the systems for biotechnological applications.
Abstract.
Author URL.
Kumar SV, Basu B, Rajam MV (2006). Modulation of polyamine levels influence growth and cell division in Chlamydomonas reinhardtii.
Physiology and Molecular Biology of Plants,
12(1), 53-58.
Abstract:
Modulation of polyamine levels influence growth and cell division in Chlamydomonas reinhardtii
We report the influence of altered polyamine levels on the growth and cell division in the unicellular green alga Chlamydomonas reinhardtii. Polyamine levels in cells were modulated by exogenous addition of polyamines and their inhibitors. PUT and SPD treatments resulted in an increased cell division and the occurrence of high frequency multiple divisions as well as the impairment of flagella formation, which was correlated with increased levels of the respective polyamines. SPM treatment has been cytotoxic. Polyamine analysis has revealed that the SPM treated cells were depleted of SPD, a possible cause of lethality. Transgenic lines of Chlamydomonas with the polyamine biosynthesis genes adc, odc and samdc were generated to study the influence of transgene over-expression and consequent metabolic alterations. Surprisingly, transgenic lines did not show any change in polyamine levels, which can be attributed to inefficient transgene expression or codon bias. Results from the experiments underline the importance of polyamines in growth and development.
Abstract.
2005
Kumar SV, Rajam MV (2005). Polyamines enhance Agrobacterium tumefaciens vir gene induction and T-DNA transfer.
PLANT SCIENCE,
168(2), 475-480.
Author URL.
2004
Narula A, Kumr SV, Pande D, Rajam MV, Srivastava PS (2004). Agrobacterium-mediated transfer of arginine decarboxylase and ornithine decarboxylase genes to Datura innoxia enhances shoot regeneration and hyoscyamine biosynthesis.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY,
13(2), 127-130.
Author URL.
Kumar SV, Misquitta RW, Reddy VS, Rao BJ, Rajam MV (2004). Genetic transformation of the green alga - Chlamydomonas reinhardtii by Agrobacterium tumefaciens.
PLANT SCIENCE,
166(3), 731-738.
Author URL.
Kumar SV, Rajam MV (2004). Polyamine-ethylene nexus: a potential target for post-harvest biotechnology.
Indian Journal of Biotechnology,
3(2), 299-304.
Abstract:
Polyamine-ethylene nexus: a potential target for post-harvest biotechnology
Post-harvest biotechnology is a fast growing field of plant biotechnology. Achievements were made in the field to delay or prevent fruit ripening and softening by genetic manipulation of ethylene and cell wall metabolism. Despite the development of transgenic plants with the desired traits, the technology has not achieved the pace due to drawbacks of the existing strategies to effectively control the developmental processes following harvest. Here the authors analyse various strategies of post-harvest biotechnology and prospects, giving special emphasis to the metabolic interactions of pathways related to post-harvest characteristics-those of polyamine and ethylene-and the engineering of polyamine metabolism as an alternate strategy for post-harvest biotechnology by carefully manipulating the delicate metabolic balance and the benefits of the newly proposed strategy over the currently used ones.
Abstract.
2003
Kashyap V, Vinod Kumar S, Collonnier C, Fusari F, Haicour R, Rotino GL, Sihachakr D, Rajam MV (2003). Biotechnology of eggplant. Scientia Horticulturae, 97(1), 1-25.
