1
|
Mahadi WSW, Wong CMVL, Rodrigues KF, Teoh CP, Lindang HU, Budiman C. Complete genome sequence data of an Antarctic bacterium Arthrobacter sp. EM1 from the freshwater lake of the King George Island. Data Brief 2024; 52:109841. [PMID: 38146304 PMCID: PMC10749255 DOI: 10.1016/j.dib.2023.109841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/27/2023] Open
Abstract
Arthrobacter sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises a cell factory for mannan-degrading enzymes, widely used in industry but also serves as a model organism to decipher its cold adaptation mechanism. Accordingly, whole genome sequencing of the EM1 strain was performed via Single Molecule Real Time sequencing under the PacBio platform, followed by genome HGAP de novo assembly and genome annotation through Rapid Annotation System Technology (RAST) server. The chromosome of this strain is 3,885,750 bp in size with a GC content of 65.8. The annotation predicted a total of 3607 protein-coding genes and 65 RNA genes, which were classified under 398 subsystems. The subsystem with the highest number of genes is carbohydrate metabolism (397 genes), which includes two genes encoding mannan-degrading enzymes (endoglucanase and α-mannosidase). This confirmed that the EM1 strain is able to produce cold-adapted mannan degrading enzymes. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at GenBank (Bioproject ID Accession Number: PRJNA963062; Biosample ID Accession Number: SAMN34434776; GenBank: CP124836.1; https://www.ncbi.nlm.nih.gov/nuccore/CP124836).
Collapse
Affiliation(s)
- Wan Shuhaida Wan Mahadi
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | | | - Kenneth Francis Rodrigues
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | - Chui Peng Teoh
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| | - Herman Umbau Lindang
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching–Kota Samarahan Expressway, Kota Samarahan, Sarawak 94300, Malaysia
| | - Cahyo Budiman
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah 88400, Malaysia
| |
Collapse
|
2
|
Abu Bakar N, Lau BYC, González-Aravena M, Smykla J, Krzewicka B, Karsani SA, Alias SA. Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus. MICROBIAL ECOLOGY 2023; 87:11. [PMID: 38060022 DOI: 10.1007/s00248-023-02311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
Abstract
In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.
Collapse
Affiliation(s)
- Nurlizah Abu Bakar
- Institute of Ocean and Earth Sciences, C308, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- National Antarctic Research Centre, B303, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Benjamin Yii Chung Lau
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Jerzy Smykla
- Department of Biodiversity, Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Krakow, Poland
| | - Beata Krzewicka
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Kraków, Poland
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- National Antarctic Research Centre, B303, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| |
Collapse
|
3
|
Feng H, Meng P, Zhang S, Chen W, Wang H, Wang C. Insights from comparative transcriptome analysis in the responses of Pb-tolerant fungi Curvularia tsudae to Pb stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114476. [PMID: 38321691 DOI: 10.1016/j.ecoenv.2022.114476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 12/06/2022] [Accepted: 12/23/2022] [Indexed: 02/08/2024]
Abstract
The fungus Curvularia tsudae can survive in environments that are extremely contaminated by heavy metals; however, the underlying molecular mechanisms of heavy metal tolerance are not clear. In this study, we determined the effects of lead (Pb) stress on the growth of C. tsudae and used RNA-Seq to identify significant genes and biological processes involved. The present study showed that C. tsudae had an outstanding resistant capacity to Pb stress and could survive at a concentration of 1600 mg L-1 Pb. Although an obvious inhibition on the growth was observed, the fungus exhibited tolerance as it continued to grow at a Pb concentration of 1600 mg L-1 for seven days. A total of 9997 (9020 up and 977 down) differentially expressed genes (DEGs) were detected in the mycelium of C. tsudae at Pb free (0 mg L-1) and Pb stressed samples. Pathway enrichment analysis identified several biological processes for managing Pb stress. Genes involved in carbohydrate metabolism tended to be modulated in response to Pb stress, while amino acids and the lipid metabolism would also be induced by Pb stress, and up-regulated genes involved in antioxidant substances and ABC transporters may be committed to high Pb tolerance. Our study contributes to the current literature on C. tsudae response to Pb stress and provides a useful reference for fungi as bioremediators in heavy metal-contaminated environments.
Collapse
Affiliation(s)
- Huan Feng
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Panpan Meng
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shouxia Zhang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei Chen
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA
| | - Chunyan Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
4
|
Growth ability, carbon source utilization and biochemical features of the new specie Zalaria obscura. World J Microbiol Biotechnol 2022; 38:229. [PMID: 36149541 PMCID: PMC9508035 DOI: 10.1007/s11274-022-03417-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022]
Abstract
This research investigated the characteristics of Zalaria obscura LS31012019 in terms of growth ability in different media (SDB, YPD and TSB) and temperatures (22, 25 and 37 °C), utilization of several carbon sources (Glucose, Fructose, Lactose, Sucrose, Xylose, Glycerol and Mannitol at 5, 2 and 1%) and several biochemical features (total protein content, Glutathione, pigments), in comparison with those of the phylogenetically related Aureobasidium pullulans ATCC 15233. The best growth of Z. obscura LS31012019 was obtained in YPD at 25 °C with the highest OD value (0.45) after 144 h of incubation, similar to that of A. pullulans ATCC 15233 (0.48). Glucose resulted the preferred carbon source for both the considered yeasts but also sucrose resulted in efficacy supporting the growth of Z. obscura LS31012019 and A. pullulans ATCC 15233, for their ability in converting sucrose to glucose and fructose and the latter into glucose. Interestingly, Z. obscura LS31012019 utilized also glycerol and mannitol. The biochemical analysis showed the similarity of protein profile in Z. obscura LS31012019 and A. pullulans ATCC 15233 (from 90 to 20 kDa) and a reduced GSH content (0.321 and 0.233 µmol/mg). The pigments extraction with hexane generated a yellow oleaginous pellet in both the strains, while a yellow solid matrix more intensely coloured in A. pullulans ATTC 15233 was visible with the following solvent extractions. Overall, our data showed that Z. obscura LS31012019 can grow in different media and temperatures and utilize carbon sources apart from glucose and sucrose, shifting to a non-fermentative metabolism. These results improve the information regarding the characteristics of Z. obscura, opening a new field of investigation for the possible application of new species of black yeasts in human application.
Collapse
|
5
|
Song Y, Hu Z, Xiong Z, Li S, Liu W, Tian T, Yang X. Comparative transcriptomic and lipidomic analyses indicate that cold stress enhanced the production of the long C18–C22 polyunsaturated fatty acids in Aurantiochytrium sp. Front Microbiol 2022; 13:915773. [PMID: 36204624 PMCID: PMC9530390 DOI: 10.3389/fmicb.2022.915773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Aurantiochytrium sp. belonging to Thraustochytrids are known for their capacity to produce long-chain polyunsaturated fatty acids (PUFAs). However, effects of cold stress accompanied with staged-temperature control on the fatty acid metabolism in Aurantiochytrium sp. were rarely studied. In this study, cold stress (15°C, 5°C) was applied for Aurantiochytrium sp., with the physiological responses (morphology, growth, fatty acid profiling) and gene expression related FA synthesis, lipid metabolism, and regulatory processes was observed. Results showed that there is a significant change for the lipid types under 5°C (251 species) and 15°C (97 species) treatment. The 5°C treatment was benefit for the C18–C22 PUFAs with the yield of docosahexaenoic acid (DHA) increased to 1.25 times. After incubation at 15°C, the accumulation of eicosadienoic acid (EA) (20:2) was increased to 2.00-fold. Based on transcriptomic and qPCR analysis, an increase in genes involved in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways was observed under low-temperature treatment. With upregulation of 3-ketoacyl-CoA synthase (2.44-fold), ketoreductase (2.50-fold), and dTDP-glucose 4,6-Dehydratase (rfbB) (2.31-fold) involved in PKS pathway, the accumulation of DHA was enhanced under 5°C. While, FAS and fatty elongase 3 (ELO) involved in the FAS pathway were upregulated (1.55-fold and 2.45-fold, respectively) to accumulate PUFAs at 15°C. Additionally, glycerol-3-phosphate acyltransferase (GPAT), lysophospholipid acyltransferase (LPAT), phosphatidic acid phosphatase (PAP), phosphatidylserine synthase (PSS), and phosphatidylserine decarboxylase (PSD) involved in glycerophospholipid biosynthesis were upregulated at 5°C increasing the accumulation of phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylinositol (PI). However, glycolysis and the TCA cycle were inhibited under 5°C. This study provides a contribution to the application of two-staged temperature control in the Aurantiochytrium sp. fermentation for producing cold stress-enhancing PUFAs, in order to better understand the function of the key genes for future genetic engineering.
Collapse
Affiliation(s)
- Yingjie Song
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zheng Xiong
- Shenzhen Institute of Modern Agricultural Equipment, Shenzhen, China
| | - Shuangfei Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wei Liu
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tian Tian
- Shenzhen Institute of Modern Agricultural Equipment, Shenzhen, China
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Xuewei Yang,
| |
Collapse
|
6
|
KINASZ CAMILAT, KREUSCH MARIANNEG, BENDIA AMANDAG, PELLIZARI VIVIANH, DUARTE RUBENST. Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection. AN ACAD BRAS CIENC 2022; 94:e20210621. [DOI: 10.1590/0001-3765202220210621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
|
7
|
Liu L, Xu S, Wang F, Yan Z, Tian Z, Ji M. Effect of exogenous N-acyl-homoserine lactones on the anammox process at 15 ℃: Nitrogen removal performance, gene expression and metagenomics analysis. BIORESOURCE TECHNOLOGY 2021; 341:125760. [PMID: 34454237 DOI: 10.1016/j.biortech.2021.125760] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
In this study, C6-HSL and C8-HSL were separately introduced into anammox biofilm reactors to facilitate the anammox performance at 15 ℃. After operation 138 d, total nitrogen removal efficiencies in reactors with amendment C6-HSL or C8-HSL at 15 ℃ reached 76.2% and 74.6%, respectively. Content of extracellular polymeric substances increased by 19.8%, 67.7% and 121.2% in control group, C6-HSL and C8-HSL addition group, respectively. Genes associated with nitrogen removal (i.e., hzo, hzsB, nirS, and ccsB) showed higher expression level at amendment C6-HSL or C8-HSL group. Metagenomics analysis found that amendment of C6-HSL or C8-HL resulted in an increased abundance of genes related to the tricarboxylic acid cycle, amino sugar and nucleotide sugar metabolism, and also genes associated with amino acid biosynthesis pathways. Overall, amendment C6-HSL or C8-HSL had been confirmed as the effective method to improve the performance of anammox bioreactor at 15 ℃.
Collapse
Affiliation(s)
- Lingjie Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Sihan Xu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Fen Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Zhao Yan
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhongke Tian
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| |
Collapse
|
8
|
Abu Bakar N, Karsani SA, Alias SA. Fungal survival under temperature stress: a proteomic perspective. PeerJ 2020; 8:e10423. [PMID: 33362961 PMCID: PMC7747687 DOI: 10.7717/peerj.10423] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Increases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role in soil ecosystems as the primary agent of decomposition, recycling of organic nutrients. Fungi also include important pathogens of plants, insects, bacteria, domestic animals and humans, thus highlighting their importance in many contexts. Temperature directly affects fungal growth and protein dynamics, which ultimately will cascade through to affect crop performance. To study changes in the global protein complement of fungi, proteomic approaches have been used to examine links between temperature stress and fungal proteomic profiles. SURVEY METHODOLOGY AND OBJECTIVES A traditional rather than a systematic review approach was taken to focus on fungal responses to temperature stress elucidated using proteomic approaches. The effects of temperature stress on fungal metabolic pathways and, in particular, heat shock proteins (HSPs) are discussed. The objective of this review is to provide an overview of the effects of temperature stress on fungal proteomes. CONCLUDING REMARKS Elucidating fungal proteomic response under temperature stress is useful in the context of increasing understanding of fungal sensitivity and resilience to the challenges posed by contemporary climate change processes. Although useful, a more thorough work is needed such as combining data from multiple -omics platforms in order to develop deeper understanding of the factor influencing and controlling cell physiology. This information can be beneficial to identify potential biomarkers for monitoring environmental changes in soil, including the agricultural ecosystems vital to human society and economy.
Collapse
Affiliation(s)
- Nurlizah Abu Bakar
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- National Antarctic Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- National Antarctic Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
9
|
Hu B, Luo M, Ji X, Lin L, Wei Y, Zhang Q. Proteomic analysis of Mortierella isabellina M6-22 during cold stress. Arch Microbiol 2016; 198:869-76. [PMID: 27262947 DOI: 10.1007/s00203-016-1238-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/29/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
Abstract
We aimed to gain a better understanding of cold adaption in Mortierella isabellina M6-22 by using proteomics approaches. The temperature range and optimal temperature for M6-22 growth were investigated, and composition changes in fatty acids were analyzed. Accompanied with the 2-D gel electrophoresis, MALDI-TOF/TOF-MS analysis was conducted to characterize alterations in protein profiling in M6-22 cultured at 30 °C for 24 h and 15 °C for another 24 h when compared with those cultured at 30 °C for 48 h. Gene Ontology (GO) cluster analysis was finally conducted for successfully identified proteins. M6-22 cells could grow well at temperatures ranging from 15 to 30 °C. As temperature decreased from 30 to 15 °C, LA and GLA significantly increased from 11.63 to 17.85 % and from 9.12 to 13.19 %, respectively, while oleic acid significantly decreased from 47.25 to 36.53 %. Proteomics analyses revealed 111 differentially expressed protein spots, among which 5 unique proteins (A38, A40, A47, A49 and A58), 29 up-regulated proteins and 10 down-regulated proteins were identified by MALDI-TOF/TOF-MS. GO enrichment analysis demonstrated that these proteins mainly involved in glycolytic pathway (A34 and A50), electron transport (A28), ATP production (A35 and B39) and protein modification (A38). A total of 44 differentially expressed proteins have been successfully identified in M. isabellina M6-22 cultured at 15 °C. These proteins may play important roles in cold adaption via regulation of ATP synthesis, activation of cold-adaptive proteins, degradation of needless protein, accumulation of PUFAs, etc.
Collapse
Affiliation(s)
- Binbin Hu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Minzhou Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Lianbing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China.
| |
Collapse
|
10
|
Jain R, Jha S, Mahatma MK, Jha A, Kumar GN. Characterization of arsenite tolerant Halomonas sp. Alang-4, originated from heavy metal polluted shore of Gulf of Cambay. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:478-486. [PMID: 26865328 DOI: 10.1080/10934529.2015.1128717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Arsenite [As(III)]-oxidizing bacteria were isolated from heavy metal contaminated shore of Gulf of Cambay at Alang, India. The most efficient bacterial strain Alang-4 could tolerate up to 15 mM arsenite [As(III)] and 200 mM of arsenate [As(V)]. Its 16S rRNA gene sequence was 99% identical to the 16S rRNA genes of genus Halomonas (Accession no. HQ659187). Arsenite oxidase enzyme localized on membrane helped in conversion of As(III) to As(V). Arsenite transporter genes (arsB, acr3(1) and acr3(2)) assisted in extrusion of arsenite from Halomonas sp. Alang-4. Generation of ROS in response to arsenite stress was alleviated by higher activities of catalase, ascorbate peroxidase, superoxide dismutase and glutathione S-transferase enzymes. Down-regulation in the specific activities of nearly all dehydrogenases of carbon assimilatory pathway viz., glucose-6-phosphate, pyruvate, α-ketoglutarate, isocitrate and malate dehydrogenases, was observed in presence of As(III), whereas, the specific activities of phosphoenol pyruvate carboxylase, pyruvate carboxylase and isocitrate lyase enzymes were found to increase two times in As(III) treated cells. The results suggest that in addition to efficient ars operon, alternative pathways of carbon utilization exist in the marine bacterium Halomonas sp. Alang-4 to overcome the toxic effects of arsenite on its dehydrogenase enzymes.
Collapse
Affiliation(s)
- Raina Jain
- a Department of Plant Molecular Biology and Biotechnology , ASPEE College of Horticulture and Forestry, Navsari Agricultural University , Navsari , Gujarat , India
| | - Sanjay Jha
- b Gujarat Agricultural Biotechnology Institute, Navsari Agricultural University , Surat , Gujarat , India
| | - Mahesh K Mahatma
- c Directorate of Groundnut Research , Junagadh , Gujarat , India
| | - Anamika Jha
- d Department of Biotechnology , Ashok & Rita Patel Institute of Integrated Study & Research in Biotechnology & Allied Sciences , New Vidyanagar , Gujarat , India
| | - G Naresh Kumar
- e Department of Biochemistry , Faculty of Science, The Maharaja Sayajirao University of Baroda , Vadodara , Gujarat , India
| |
Collapse
|
11
|
Joshi R, Karan R, Singla-Pareek SL, Pareek A. Ectopic expression of Pokkali phosphoglycerate kinase-2 (OsPGK2-P) improves yield in tobacco plants under salinity stress. PLANT CELL REPORTS 2016; 35:27-41. [PMID: 26408146 DOI: 10.1007/s00299-015-1864-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 08/29/2015] [Accepted: 09/03/2015] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE Our results indicate that OsPGK2a-P gene is differentially regulated in contrasting rice cultivars under stress and its overexpression confers salt stress tolerance in transgenic tobacco. Phosphoglycerate kinase (PGK; EC = 2.7.2.3) plays a major role for ATP production during glycolysis and 1, 3-bisphosphoglycerate production to participate in the Calvin cycle for carbon fixation in plants. Whole genome analysis of rice reveals the presence of four PGK genes (OsPgks) on different chromosomes. Comparative expression analysis of OsPgks in rice revealed highest level of transcripts for OsPgk2 at most of its developmental stages. Detailed characterization of OsPgk2 transcript and protein showed that it is strongly induced by salinity stress in two contrasting genotypes of rice, i.e., cv IR64 (salt sensitive) and landrace Pokkali (salt tolerant). Ectopic expression of OsPgk2a-P (isolated from Pokkali) in transgenic tobacco improved its salinity stress tolerance by higher chlorophyll retention and enhanced proline accumulation, besides maintaining better ion homeostasis. Ectopically expressing OsPgk2a-P transgenic tobacco plants showed tall phenotype with more number of pods than wild-type plants. Therefore, OsPgk2a-P appears to be a potential candidate for increasing salinity stress tolerance and enhanced yield in crop plants.
Collapse
Affiliation(s)
- Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ratna Karan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Sneh L Singla-Pareek
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
12
|
Kashyap PL, Rai A, Singh R, Chakdar H, Kumar S, Srivastava AK. Deciphering the salinity adaptation mechanism inPenicilliopsis clavariiformisAP, a rare salt tolerant fungus from mangrove. J Basic Microbiol 2015; 56:779-91. [DOI: 10.1002/jobm.201500552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/11/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Prem Lal Kashyap
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
| | - Anuradha Rai
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
| | - Ruchi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
| | - Sudheer Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
- ICAR-Indian Institute of Wheat and Barley Research; Karnal Haryana India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms; Mau Uttar Pradesh India
| |
Collapse
|
13
|
An ENA ATPase, MaENA1, of Metarhizium acridum influences the Na + -, thermo- and UV-tolerances of conidia and is involved in multiple mechanisms of stress tolerance. Fungal Genet Biol 2015; 83:68-77. [DOI: 10.1016/j.fgb.2015.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 11/24/2022]
|
14
|
Ma Z, Tan Y, Cui G, Feng Y, Cui Q, Song X. Transcriptome and gene expression analysis of DHA producer Aurantiochytrium under low temperature conditions. Sci Rep 2015; 5:14446. [PMID: 26403200 PMCID: PMC4585886 DOI: 10.1038/srep14446] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/28/2015] [Indexed: 01/05/2023] Open
Abstract
Aurantiochytrium is a promising docosahexaenoic acid (DHA) production candidate due to its fast growth rate and high proportions of lipid and DHA content. In this study, high-throughput RNA sequencing technology was employed to explore the acclimatization of this DHA producer under cold stress at the transcriptional level. The overall de novo assembly of the cDNA sequence data generated 29,783 unigenes, with an average length of 1,200 bp. In total, 13,245 unigenes were annotated in at least one database. A comparative genomic analysis between normal conditions and cold stress revealed that 2,013 genes were differentially expressed during the growth stage, while 2,071 genes were differentially expressed during the lipid accumulation stage. Further functional categorization and analyses showed some differentially expressed genes were involved in processes crucial to cold acclimation, such as signal transduction, cellular component biogenesis, and carbohydrate and lipid metabolism. A brief survey of the transcripts obtained in response to cold stress underlines the survival strategy of Aurantiochytrium; of these transcripts, many directly or indirectly influence the lipid composition. This is the first study to perform a transcriptomic analysis of the Aurantiochytrium under low temperature conditions. Our results will help to enhance DHA production by Aurantiochytrium in the future.
Collapse
Affiliation(s)
- Zengxin Ma
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanzhen Tan
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
| | - Guzhen Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
| | - Xiaojin Song
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao, Shandong, China
| |
Collapse
|
15
|
Paul S, Aggarwal C, Thakur JK, Bandeppa GS, Khan MA, Pearson LM, Babnigg G, Giometti CS, Joachimiak A. Induction of osmoadaptive mechanisms and modulation of cellular physiology help Bacillus licheniformis strain SSA 61 adapt to salt stress. Curr Microbiol 2015; 70:610-7. [PMID: 25561404 DOI: 10.1007/s00284-014-0761-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/10/2014] [Indexed: 01/24/2023]
Abstract
Bacillus licheniformis strain SSA 61, originally isolated from Sambhar salt lake, was observed to grow even in the presence of 25 % salt stress. Osmoadaptive mechanisms of this halotolerant B. licheniformis strain SSA 61, for long-term survival and growth under salt stress, were determined. Proline was the preferentially accumulated compatible osmolyte. There was also increased accumulation of antioxidants ascorbic acid and glutathione. Among the different antioxidative enzymes assayed, superoxide dismutase played the most crucial role in defense against salt-induced stress in the organism. Adaptation to stress by the organism involved modulation of cellular physiology at various levels. There was enhanced expression of known proteins playing essential roles in stress adaptation, such as chaperones DnaK and GroEL, and general stress protein YfkM and polynucleotide phosphorylase/polyadenylase. Proteins involved in amino acid biosynthetic pathway, ribosome structure, and peptide elongation were also overexpressed. Salt stress-induced modulation of expression of enzymes involved in carbon metabolism was observed. There was up-regulation of a number of enzymes involved in generation of NADH and NADPH, indicating increased cellular demand for both energy and reducing power.
Collapse
Affiliation(s)
- Sangeeta Paul
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 10012, India,
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Tang X, Feng H, Zhang J, Chen WN. Comparative proteomics analysis of engineered Saccharomyces cerevisiae with enhanced biofuel precursor production. PLoS One 2013; 8:e84661. [PMID: 24376832 PMCID: PMC3871657 DOI: 10.1371/journal.pone.0084661] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
The yeast Saccharomyces cerevisiae was metabolically modified for enhanced biofuel precursor production by knocking out genes encoding mitochondrial isocitrate dehydrogenase and over-expression of a heterologous ATP-citrate lyase. A comparative iTRAQ-coupled 2D LC-MS/MS analysis was performed to obtain a global overview of ubiquitous protein expression changes in S. cerevisiae engineered strains. More than 300 proteins were identified. Among these proteins, 37 were found differentially expressed in engineered strains and they were classified into specific categories based on their enzyme functions. Most of the proteins involved in glycolytic and pyruvate branch-point pathways were found to be up-regulated and the proteins involved in respiration and glyoxylate pathway were however found to be down-regulated in engineered strains. Moreover, the metabolic modification of S. cerevisiae cells resulted in a number of up-regulated proteins involved in stress response and differentially expressed proteins involved in amino acid metabolism and protein biosynthesis pathways. These LC-MS/MS based proteomics analysis results not only offered extensive information in identifying potential protein-protein interactions, signal pathways and ubiquitous cellular changes elicited by the engineered pathways, but also provided a meaningful biological information platform serving further modification of yeast cells for enhanced biofuel production.
Collapse
Affiliation(s)
- Xiaoling Tang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Huixing Feng
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianhua Zhang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
| |
Collapse
|
17
|
Krumova ET, Stoitsova SR, Paunova-Krasteva TS, Pashova SB, Angelova MB. Copper stress and filamentous fungus Humicola lutea 103 — ultrastructural changes and activities of key metabolic enzymes. Can J Microbiol 2012; 58:1335-43. [DOI: 10.1139/w2012-112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Humicola lutea 103 is a copper-tolerant fungal strain able to grow in the presence of 300 μg·mL–1 Cu2+ under submerged cultivation. To prevent the consequences of copper overload, microorganisms have evolved molecular mechanisms that regulate its uptake, intracellular traffic, storage, and efflux. In spite of this avoidance strategy, high heavy-metal concentrations caused distinct and widespread ultrastructural alterations in H. lutea. The mitochondria were the first and main target of the toxic action. The effect of copper on activities of the key enzymes (hexokinase, glucose-6-phosphate dehydrogenase, malate dehydrogenase, and isocitrate dehydrogenase) included in the 3 main metabolic pathways, glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle, was investigated. High metal concentrations exhibited a dramatic negative effect on hexokinase, while the other 3 enzymes showed a significant and dose-dependent stimulation. On the basis of the present and previous results we concluded that the copper-induced oxidative stress plays an important role in the fungal tolerance to high Cu 2+ concentrations.
Collapse
Affiliation(s)
- Ekaterina Ts. Krumova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Academician G. Bonchev, 1113 Sofia, Bulgaria
| | - Stoyanka R. Stoitsova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Academician G. Bonchev, 1113 Sofia, Bulgaria
| | - Tsvetelina S. Paunova-Krasteva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Academician G. Bonchev, 1113 Sofia, Bulgaria
| | - Svetlana B. Pashova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Academician G. Bonchev, 1113 Sofia, Bulgaria
| | - Maria B. Angelova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Academician G. Bonchev, 1113 Sofia, Bulgaria
| |
Collapse
|